Just bought a bone stock '87 Honda TRX250R that has a K&N on it and no air box lid. I bought a FMF SST Pipe for it, and silencer. I will be riding this quad at glamis, 35:1 oil ratio, 92 octane fuel(sometimes 50/50 mix of 92 and 103 octane).

What main and slow jet should I run?.....or at least start with?

Thanks!

stock main jet is a #152
stock slow jet is a #48
jet needle in the 3rd groove

Now that your adding a pipe and silencer it is best to start off going @ 4 jet sizes higher. This will most likely make it rich. do some plug chops and work your way down 1 jet size at a time.
Usually the slow jet doesn't need to be messed with for just a pipe change. Modified port timing and port enlarging will have an effect on the slow jet as well as al the other jetting issues in the carb.
Once you get your jetting set on flat land, go up to the next larger size main jet. this will keep you from seizing the engine up a long WOT climb on the dunes.
Remember this, with all two strokes the more load you put on the engine the leaner the mixture becomes so you have to increase the amount of fuel needed to cool and lubricate the cylinder walls. Its always best to change out a $2.50 spark plug than spen big bucks replacing parts on a siezed engine.

Dune Nazi is on the money.

Always start with bigger size jets and work your way down.
NEVER start lean and work your way up. This is a ticket to the shop.

You should start 4 jets sizes up.
Although you mention you run 35:1 (richer than 32:1).

My guess is that even after you start 4 jet sizes bigger, you may end up with just 2 sizes bigger to compensate your gas premix.

Thanks guys! Another question, if I ran a higher octane fuel, like a 50/50 mix of 92 octane and 103(or whatever that race fuel that some 76 stations have), would my bike run leaner or richer than running just 92 octane. Thanks!

The experts say no. And I have not noticed any difference.

Now when you use VP, that's a different story. If you don't believe me, try the following:

1) Run regular pump gas (any octane rating) and touch the carb.
Is it cold? the answer is NO.

2) Now run VP all by itself(with 2-stroke oil of course). Now touch the carb.
Is it cold? Hell YES!

If temperature changes affects how rich or lean your mixture is, the same theory applies with VP. I usually end up using 2 size smaller jets when running VP.

How do I know if this 250R quad that I bought needs a new top end? Any easy ways of checking? What are the tell tail signs that it needs to be replaced?

A compression check will tell you a lot, otherwise you could just pull the head off and inspect it.