I just rebuilt my topend busted the old piston.I didnt run any thrust washer on it.Well i had it bored to .80 also had my head milled .20.Also had some trail port done.That i end up cleaning up. Not the best in my opion.I finally got my hours in on break in and opened it up for the first time this afternoon. Big question is since i ported the motor will it need more gas by rejetting it or will i have to go down. Also shaving the head would the jetting have to go up or down.It seem the  Blaster everything you do to them it seems you go up in jets.Seem like you go down on the Lts.Im confussed on this.I  rejetted before i started it i was lean before it blew because of the cold.But it ran like crap when i open it up.Its  rich or the power valve nots right.Had this problem last rebuild. Which it was the power valve..But is it up or down on the jetting on  lt250r when doing mods.Help  me please.Thanks in Advance Brian

You need to sort out one jetting circuit at a time.

What is not running right exactly?

Will it idle on it own? What about half throttle? How does it run? Full throttle? 

ride bike with 1/4 throttle, then see what it does. does it rev up, bog down or hold steady rpm.
try that at half then 3/4 this will help you find the right jets you need to be running. then try doing a plug chop
once you get closer to where it should be running

not sure of all the history on the machine but I just got done replacing a lot in the clutch side of the motor, specifically  the power valve actuator and the ball bearings behind it. if either is out of spec it can tie up everything. also check those damn plastic clips on the rod. they like to break and get wedged in the clutch cover. just a few things to check while you're in there.

When the old piston went bad it broke above the exhaust port.Most of it got above the piston and went up in the head.Their was a piece i couldnt find.Split the case it wasnt in the bottom of the motor.Well i put it back together and then i got my head back threw the power valve in and move it .The spring moved and power valve didnt but i didnt really check it.Just felt the spring move didnt watch it from the bottom and put it back on.When i took it back off that piece of piston was behind smashed  it.So i took it back of and grind the piece out which i thought i got it .I put it back on and it still hung up.So i took it off again and really took my time grinding and polishing it up.Now it work great and the bike runs great.I need to throw my 38 pwk and get
 a better pipe for it to finish it off.Saving my money for a new paul turner mid range pipe. 

i'm running a SCP/Q pipe and i agree. IMO best pipe hands down for a 250.

maybe put the powervalve in there without the bearings or anything and see how it moves in the cylinder. clean it up, check to see to bearings are straight on the pv. oil it up a bit. and polish a bit too never hurts.