[BoBO]

It depends on what stage your jet kit is. For example, I have a stage 2 dynojet kit so I keep my stock airbox and just have an aftermarket filter and slipon.

But for more power improvements I would just leave the bike as is until you get the 650 running again. The only power you are going to notice is when you start working on the engine internals such as: increasing compression or boring out the block to increase displacement in conjunction with carb tuning.

I wouldn't expect much from a 250 in terms of power. A good running 250 with a smooth idle is more rewarding. Adding aftermarket exhaust and jetting will definitely improve power but mostly on the top-end.