I used 01 XCR800 on mine. I used a set of phazer manifolds and had to open them up a little bit with a cartridge wheel. I used brass hex head pipe plugs to fill the boost bottle hole. I also had to slot the end manifolds about the 1/8 " mentioned. The throttle response was amazing with those 38s. I burnt the mag and pto pistons down last year with 390 mains and 50 pilots. ( I believe I also had air in the cooling system). I have the needle in the third position and the airbox in place modified to fit on the carbs (no shelf). The motor has lake race ported cylinders, Vforce2 reeds, Mountain Perf Viper head with 21cc inserts, and CPR pipes ceramic coated.
I found the 50 pilots to be way to rich. You will need to drop down to 45s. I currently have 410 mains in it right now and the needle in the 4th position and the plugs are colored real nice. I am going to jump up to 420s for a little while to see if they are to rich. I burnt down again on my last ride due to air in the cooling system. The Mountain Perf viper head is real hard to get all the air out of. I just didn't have time to check it real well. Oh well new piston and relating again.
The TPS was a bit tricky, don't have to change the wires, but you do have to rotate the TPS to the other end of the adjustment. The resistances on the two outer wires oppose each other. One goes up and one goes down, just crank it the other way and it should be good. The throttle pull on the Polaris carbs is a little different; therefore you cannot get the same range as the Yamaha TPI. The best way to do it is to set your idle at the speed you want it then set the TPI adjustment at the point just after the check engine light goes out. The light will flash like 3 times to tell you there is a problem with the TPI. If you want to tolerate the light flashing at idle, set the ohm range to the WOT settings. If you don't want to see the light flashing, just adjust to the point the light goes out at idle. It’s not off that far at WOT.
You will have to change the cable length. Hope you have a bike shop that can put a new lead end on it.
The fuel bowls are deeper in the Polaris carbs. You will have to cut the bowl drains off and epoxy them closed. The Polaris carbs have two fuel inlets to feed the three carbs. They are T'd between them so you will have to plug one supply line or t two together (that's what I did).
I now have UNI filters on mine. At idle with the airbox in place my EGTs were off a little bit. With the airbox off they were all close to the same. The mag carb appeared to be getting less air since the shelf is no longer directing air right to it. I figured there was no point using the stock shelf since it was designed to supply air to the smaller 33s.
My next purchase is going to be a 01 SRX CDI. Oh yeah and make sure I have all the air out of the cooling system. Even with the rear heat exchanger, 165 hp needs all the cooling it can get. The motor sure sounds nice spinning at 9100rpm too. That’s everything I could I think of that was a pain in the butt.