I recently did a 73mm top end rebuild on my 97 trail boss 250. The thing sat for a few years before I ran it for about 20 minutes and it blew a hole in the piston. The reason was running lean from the intake adapter being broken. Fast forward to today, I just completed the top end rebuild and its running pretty rough. It wants to stall at idle, and when u rev in neutral the revs hang, and sometimes they go higher. I have no idea where to start. It seems to run pretty good when it's moving but stop and it wants to stall. Going from neutral to reverse for forward is a pita, as it wants to stall, then u blip the throttle and the revs shoot up and hang there. Also where is the bleed screw for the injection pump? It it the big hex head/phillips screw? Another thing, it doesn't rev as high on long straits as it does in neutral, top speed is prolly around 35. Can someone point me into the right direction?

Also what size is the crankcase drain bolt?, I seem to have lost it

You rebuild the carb?

Problem is most people over look the bottom end especially crank seals,rod and crank bearings. You take a chance just on doing the top end only. Oil pump bleed screw is the the hex 10 mm bolt on top of the pump. Along with checking out the carb,the most common crank seal to fail is the one behind the front clutch.It could be sucking air, leaning out the fuel/oil mixture.I'd replace both seals at least or you could damage another piston.

Yea, I plan on the crank seals, I just wanted to get it running first. Here's what I did today: found and reinstalled the crankcase drain bolt, semi-cleaned the carb, and tightened the base bolts a tad more. I also bled the oil injection. She runs great and idles great now, but the top speed is lacking. I noticed at the bottom of the throttle on the handle bar has a slotted throttle stop, and its only letting it open a little more then half way. Is this the top speeed limiter?

This is the throttle limiter,but I still stress crank seal replacement on an old machine at least before any thing major happens! I've had many,many brought back into the shop after people have just brought in cylinders for me to bore and neglected the bottom end and ended up throwing good $ down the drain when a piston holed or seized! It's the same to me as just rebuilding one head only on a V8 engine when a top end is only done on a 16 year old two stroke!!

Well I just ordered the new crank seals and will be doing that and clutch springs. I think my front brakes are dragging, what could cause that?

Worn out pads that allow the caliper pistons to travel too far can cause sticking along with caliper pistons themselves needing new seal kits,or the master cylinder itself needing a new piston/seal kit.Dirt Cheap Yamaha, Honda, Arctic Cat & Polaris OEM Parts & Accessories – Cycle Parts Warehouse http://www.cyclepartswarehouse.com/f...1997&fveh=5428 Plus you can try a general clean up and fluid flush first to see if it helps.Some times all you have to do is push the caliper slides back in and bleed the system.

I was looking at the 2nd link you posted, its a rebuild kit minus the piston? What's the likeliness of the piston being bad? These front rotors are gouged and rough looking. The brake pads were replaced a few years ago but he didn't do the rotors. Also, I think that's my top speed problem, it just feels like something is holding it back. Either the trans is slipping or its the brakes. I don't think it's the trans as I can ride a good wheelie easily, and it gets to speed fairly quick. Ride on a flat surface and let off the throttle and it slows pretty quick. Also I can hear a metal on metal squeel at slow speeds and slow sharp turning

Look closer at the breakdown. Item # 8 is the complete rebuild kit with the piston. Rotors can't be turned like on a car,they have to be replaced if badly scored to where they can't just be sanded down a little.Think you need to pull the calipers to see what's going on..