Hi I recently purchased a 98 900rr and on the second day it dropped a valve so I have been searching for a replacement engine and I came across a really sweet deal on a 96 engine so now I have got the engine in the bike and got some questions with the cooling system.... On my 98 there was a thermostat on the head and the hose came out of there and went into another housing with another Thermostat then went to the Water pump the issues that im seeing with the 96 engine is that there is a thermostat on the head with the neck pointing to the outside of the bike with a hose going straight to the Radiator and one hose coming out of the opposite end of the head going to the water pump... What I need to know if the second thermostat that was used on my 98 can just be eliminated all together and just keep it like it is on the 96 engine and if there is any other problems that some of you guys may have experienced with a similar swap any info will be greatly appreciated

 

I'll bite-

Kinda...
I have the same problem, but I think there is a bit of misunderstanding going on here too.
The thermostat is on the right side under the carb rack, and the hose goes right to the right side of the radiator (rad). Then, coming out of the other side of the rad is the same size hose going to the outside fitting on the pump. Then, the inside fitting (closest to the engine) goes right back to under the headers into the case. Right? These are the only hoses that are 1 1/4" or so. Are you thinking there is a thermostat on the front of the engine under the headers?
Ok- next, the smaller lines coming off of the pump- the small fitting that points straight away from the bike, goes up to the right side under the carbs, towards the thermostat- and then the slightly larger one goes straight up, and then to the left side of the engine under the carbs as well right? (I think this is the line you want to remove. Correct?
I'm in the same boat, as I went from 96 to 97 and have the different water pump too... The bike is overheating, so I'm going back to my stock rad, and I'm contemplating changing the pump back out to the known good one. But I don't want to omit that hose if it's nesecarry!!!
If no one chimes in here before I Find out, I'll pass the info along- or some clear pics of what I got going on- it's probably the exact thing on yours??