The parts from the later TTRs will fit your TTR just fine.
The Wiseco will fit your bike. Used one myself a few years ago and it worked fine. I now use the Wossner piston kits as they are quite a bit cheaper here in the UK.
Don't forget to change the valve stem oil seals at the same time as you do the rest of the work
I decided the cilinder restoration after opening the engine to review the state of the cilinder head.
The initial problem was the engine was increasingly difficult to start. Reading the forum I've seen others also having this problem so I'll comment a bit on this.
After checking other causes (electrical, fuel feed, etc) it resulted the engine had very low compression. As fuel ignition has two prerequisites: a spark AND enough compression, difficult start can be related to deffective starter, ignition or fuel feed and/or not enough compression.
Side note: lacking a pressure gauge, an indication of low compression is the starter motor reving higher and more rapidly than normal. A quick sense of this, having an engine working fine, can be experienced operating the starter with the spark plug removed.
Previously, my TTR engine was operating fine, no strange noise and normal oil consumption. So the issue probably had to be in the valve train which effectively was due to carbon build up, deteriorated valve seats and stem oil seals hardened as rock. Conclusion: the cilinder head gone to a specialist shop for complete restoration.
Doing a compression check each time cleaning/replacing the spark plug can help detecting cilinder head deterioration. The reading should be at least 150psi.
About the piston kit, the engine has around 30.000 miles on it and presumably an amount of wear that I think justifies also doing the cilinder restoration at this time. I have a Wiseco dealer in town so I think I'll go that way. It's nice to know you've had good results using them.