Ok, can't be crank key i suggested or would still be kicking back & not starting. Hope she carries on good. Oring? is that the small one for the carb. Would stay running faulty if that wasn't sealing in the bowl base. So doesn't sound like that's causing ya problem seeing it came right. Has exhaust been mentioned. If lumps of carbon get stuck in the baffle it can cause it 'Not' to rev out. Then the lumps drop out when motor isn't powering hard & blowing hard out the back. Had it happen on my yamy 100. Down the road flat out then went to half power & revs. Stopped the motor & restarted & was ok for a bit. Next time it did it i pulled the baffle & a round lump of carbon was stuck right in the end. Mind you was a small baffle so easily blocked.

Thanks! Though it could be exhaust so I’ll have to remove that and check it out. Maybe try and get some compressed air blown through and see if anything falls out. 

Removed exhaust, shook it blew air through it. Not really any rattling or anything coming out so I re installed. Ordered cap seals. Carb O-ring, bowl gasket l, exhaust gasket and new exhaust spring. Still looking for the o-ring that presses against intake manifold. I want to get this one running proper before I start either my ct1 or dt125e I’ve been itching to get after those guys 

The ebay item id given is invalid, no result has been senta pair on ebay right now, one cheap, one three times more.

Apparently we don't like posting ebay links? Go on ebay and search the Yamaha part number: 93210-37140-00
It should bring them up.
 

Thank you I found one! Don’t really want to pay $15 for a o-ring :( but that’s how it goes.  so it won’t rev past 4K so I checked if removing air filter would help. It did slightly I got to 5k but I’m really excited to see if that main jet o ring I ordered will help my problem. Its still really kicking back on me so does that mean timing is wrong? 

Not easy to be far from right on those. So without keeping on about crank key which did you say was ok!!, then a very wide points gap could do it, but too too wide & it won't run as won't be shutting fully. Timing by memory is 3.2mm btdc on a 250. Not a lot do do with not wanting to rev though. Hope the Oring sorts that.

Did not check crank key as I’m not entirely sure what that entails but I will do some research, hoping points are easy access as well 

Oh, thought you had, so better do that. Need a special puller [cheap as chips to buy] 27mm left Hand thread. If the flywheel has moved its likely the nut will be not very tight so hold the flywheel by hand & see if you can undo the nut. Ebay 384150798052 should be a suitable puller. Remember its left thread when screwing it in. Take both washers out behind the nut to get it screwed well in--right in all the way. Keep centre bolt backed way out so it doesn't contact the crank before you get the puller fully home. Fine thread that 27 & easily pulled out of the flywheel.

Perfect yes I have a puller so shouldn’t be a problem. For the timing I see in the manual it has this gague you stick on the top to measure how far you are from tdc. I’m hoping and guessing you don’t actually need one of those and there’s an easier way to check it? 

There is no easier way to check, you need a dial indicator gauge to check for tdc.  They are not that expensive...