If you have a 1981 thru 1990 JS-440 or JS-550 it most likely has an iron - or - solid steel cylinder unlike earlier and later models that have alloy cylinders with steel sleeves.  Some of you may have an aftermarket cylinder or maybe a swapped out alloy cylinder - if that is the case - please see the  - SX - 550 water lines memo that is nearby and follow that system. 
 
If  you have one of these all iron cylinders and you want the boat to live - then your going to need to install a proper water line set up - or - modify what you have - as many already have a second water line installed.   Just because you may have ridden the ski for some time and had no problems - does NOT mean this does not apply to you.  You may have “gotten away with it” for years - but - luck only lasts so long. 
 
I invented the first “dual water line” system used in JS units and improved on that system constantly for many years after that. The following is what I have found to be the best and most reliable of the 25 or so different systems we tried.  I trust dual water lines over a single larger water line ( ½ to ¾ inch ) because I feel the chances of something clogging one line are quite good - but - something clogging 2 lines is not so good.
 
First you need to buy your water lines - (2)  - yes two !   Do not attempt to use the stock water line for two reasons - first - it snakes through the hull and the chances of it being kinked or damaged is very real. Second - when you drill a new hole through the hull - your chances of hitting that water line are VERY good.  When you hit -or even just nick- that water line - it will leak water into the foam inside your hull and your hull will very soon weigh about another 100 pounds - eventually it will swell up the ride tray and break the hull. Drying out a water soaked hull is nearly impossible. Don’t go there.   Two nice stainless 3/8^th inch water tubes are best - but - kind of hard to find.  You can use 3/8^th  copper tube - available at most any home or auto store.  Once you have these - find a drill bit that is ever so slightly larger than the outside of the tubing you bought - try to buy a “step” drill bit - where the part that goes in the drill is smaller than the bit itself.  Then find a welder - your going to want him to weld a 36inch solid rod to the end of the drill bit - the welder should have some in stock - if not he will send you to the place you need to go and buy it.  If the drill bit is a “step” drill bit the weld should not be larger than the drill bit - if it is - some grinding may be needed.  If the drill bit and the rod are the same size - it will have to be ground down to very near flush or the drill will not proceed through the hull.  Some people have been able to buy 36inch long drill bits “off the shelf”  - but they are VERY pricey. 
 
With your two water lines and long drill bit in hand - it is time to begin.  The motor - battery and pump should be removed.  Carefully drill a new hole just above the existing water line - the water line is the higher one up - the lower one ( nearly at the bottom of the hull )  is the bilge line.  Run the long drill bit through the hull at the pump area and through  the foam and the bulkhead - try to stay low so as not to hit the electrical box and aim a small bit to the outside of the hull so you miss the drive shaft area. 
Run the drill bit in and out a few times to “clear” the new passageway.  Then drill the water line on the other side of the hull as close to the area as the one on the stock side as you can get - duplicating what you did on the stock side.  Push in the new water lines.  These lines need to stick out in the pump area about 2 inches - plenty to install a rubber hose and hose clamp. They can extend into the hull as far as you wish - I always ran them up close to the electrical box for easy access.  The original stock line needs to be cut off and plugged- silicone or whatever you prefer can be used - just seal it off.   The new water lines should be sealed also - again - whatever you prefer is probably OK - I used clear silicone ( waterproof  aquarium type ) and put some around the pump area tube and slid it forward to get a seal around the outside of the new tube - the motor compartment sealing is not that critical - as it should not be under water.
 
 Look - I said it should not be - I did not say it never happens J 
 
OK - water lines thru the hull and sealed up.  Now we drill and tap a new water “pick up” on the opposite side of the pump as the stock one.  Remove the original brass fitting - a 90 degree - 1/8^th inch pipe thread fitting - and take it to the auto parts store and buy another one as close to the original as you can get.  Then buy a tap there also.  The tap will tell you the drill bit size needed - buy one if you do not have one.  Carefully mark to drill the other side of the pump.  This new pick up needs to be close but NOT exactly where the original is - just on the other side - pay attention to pump vanes and stainless steel liners - you do NOT want to drill through them or even too close to them.  On a 440 pump the new hole will be in a similar spot on the opposite side from the original so that both lines will be low - but not so low they would hit the ride plate - but - on opposite sides.  This way the flexible rubber hose is less likely to kink.  On a 550 pump the pick ups are higher up and just avoiding a vane is the main issue.  Drill and tap the pump for the new water pick up. Then drill the inside of the brass fittings out as much as you feel comfortable doing.  You may find that some of these are poorly drilled and the actual hole inside where the water is to change direction may only be 1/8^th inch.  Drilling them out is huge. Remember when working with round things pi comes into play. A ½ inch hole will flow 3.1416 times the water that a 1/4^th inch hole flows.  It is very easy to double the water flow - right here.  Install the drilled out brass fittings into the pump and then install the pump.  A trick to installing the pump is use an ice pick to push in the grease fitting sealing ball in the back - it will let the air out and the pump will slide forward with ease. You can re-use the stock water hose on one side and you will need another about the same length for the opposite side.  Re-connect the bilge line and reinstall the ride plate and intake grate. 
 
Now comes the part that will most likely throw you for a loop -
 
There are 2 ways to run these lines - one is through the head - but - the best way is through the cylinder on the intake side.  We will do the cylinder head way first as this is the most acceptable way on a 440.
 
 
Your head may have 2 brass fittings on the top very close to the spark plugs  - if not - there will be freeze plug like plugs near the spark plug holes - just outside of the spark plug holes and in the same front to back line. If you have the brass fittings in the head already - simply remove them and install 2 new brass “barb” type fittings in the head.  If you have the plug type - remove the head - and drill and tap - using the drill and tap you used on the pump to make new water inlets.  Install new straight brass “barb” fittings.
 
To do it the 550 way - or - the best way - remove the  head and cylinder  and locate the water jacket area just above the intake ports.  This is a very small area - and - the very reason we are going to this trouble.  The water jacket area is about 2 inches wide and about an inch high and less than a ½ inch deep in that area just above the intake ports.  Drill and tap a hole above each intake port where it will allow the water to enter in this small area. This should be about a half an inch below the head to cylinder surface If your running dual carbs you will have to use 90 degree fittings here - and you will need to drill these out as you did the pump 90 degree fittings - if your running single carb or stock use straight barb fittings.  Same drill and tap as the pump.  Install the new brass barbs and reinstall the cylinder and the head.
 
Iron cylinder 550 motors have VERY weak cylinders.  The mere act of torqueing down the head warps the cylinder.  Frankly to do this proper a cylinder needs to be placed into a jig and torqued down proper - and THEN honed.   The studs are so close to the cylinder to piston surface that over-bores past 1mm are foolish.  Add to this the fact that steel does NOT  dissipate heat worth a crap.  Try this - take a foot long piece of alloy and a foot long piece of steel  -  hold one in each hand - have a friend put a torch to the opposite end of these two chunks and have him heat up them both equally. You will be dropping the alloy chunk in a heartbeat - but - you will be able to hang onto the steel piece for a long time.  Just how it is.  Because there is almost no water jacketing on the intake side and because the hottest part of any motor is near the top of the cylinder - THIS is  where the coldest water needs to be.  The stock way of warming it up - by running it into the exhaust manifold first is not a good idea.  That factory “in” line is going to be our “out” line.  The exhaust getting warm is just fine - very good for power in fact.  But - the cooler any 2 stroke runs ( to a point )  the more horsepower it will make and the snappier it will be.
 
SO - connect the new water lines to the new water inlets at the head or cylinder -            re-check all the hose clamps and flexible rubber hoses and you have a dual water line system from the pump to the motor.
 
Now we have to get the water out J
 
 
 
 
 
 
The stock fitting at the front of the head is best to use to run to the exhaust system. The head gasket keeps a lot of the water up in the head and slows down the water flow which will be quite a bit faster in the more open cylinder and exhaust manifold area.  SO - it is a steady and warmer supply.  Most of you will have restrictions of some sort to keep from pouring too much water into the exhaust system.  Use of “T’s” and “bypasses” are common and fine - just be careful not to overheat the water box or muffler. I prefer a “T” in the line from the head to the pipe and the use of restrictors from the “T” to the pipe to regulate how much water my exhaust system gets and a “pisser” out the right side above the hull bond line - so it can be seen to check that water is flowing and to get the excess water out.  The factory ( or aftermarket ) fitting at the bottom of the exhaust manifold is the other “out” line.  Be sure to route it out of the hull BELOW the fitting at the manifold so ALL the water can drain out of the motor when it is shut down. 
 
This iron motor is responsible for selling more Yamaha’s than any other one item.  And as you have noted - I am very critical of this design.  However - if you will install this reverse flow - dual water line system  - you can get a lot of life out of one of these motors.  God knows they make good power ( especially 86 through 90 models ) and they are fun.   This cooling method will make your stocker or your mod live and it can be done on the cheap and in one day with parts available most anywhere.  By your third one - you should have it down to about a 2 hour job.
 
Hope this helps J
 
By Cliff Jones