Jha have been building NSR's for a long time, so they know what's going on.
Harc-Pro are (or at least were) big fans of strokers and can also build a quick NSR.
I used to work for Harc, so I'll have to recommend them if you want any tuning work done.
Most of the missing power on the NSR is in the exhaust port. It's too small to make any real power, but just cleaning up all the nasty over hanging nikasil plating can make for a better engine, more power and more rpm.
I gather you have a set of cut cylinders now so it'll be interesting to see how they go.
Unless there's been any changes, Harc pipes should be good for peak power around the 11000 mark, with over rev up to 12500, which in my opinion makes for a better ride around faster tracks than older Jha designs which peaked lower, but gave better mid range.
If you want to compete on equal terms then you'll really have to start looking at a full SP Race set-up. Talk to the guys with the faster bikes and see what they're doing.
Removing kickstart, 2T oil pump etc all give tiny power increases, as well as losing weight. Some say don't take 'em off, but it's a race bike, get rid of them!!
How about going total loss ignition? If regs state that you don't have to have a charging ignition then you can remove the stator so no magnetic frictional losses. Then heat up the flywheel until the glue holding the magnets in melts and flick them out. Instant super light flywheel. Just make sure you've got a good condition, freshly charged battery at the start of every session. Should be goof for at least half an hour.
I'd throw the airbox too, but fit an HRC type air box, or make something similar.
Oh well, let's see how you get on with the new barrels first.