Hi,
I had the same problem with mine
I'm running a '82 TR1 with a standard air filter, standard jets and settings and Jama headers with trumpet megaphones
I'd stripped and cleaned the carbs, fitted new diaphragms, jets, needles, air screws and float needles
I've junked the mixture control valve (as its function is purely for emission control, not smooth running)
It would start ok but took a bit to warm up
on small throttle openings it would miss and sputter and on closing the throttle it would spit and bang
Haynes and other manuals don't give a setting for the pilot air screw
I read somewhere 3 turns out, and somewhere else 4 turns
I tried both but it was no better.
I found an interesting article about setting Hitachi carbs here
http://www.drpiston.com/hitachicarbs.htmlSo at Dr Pistons suggestion I got a Gunson Colortune
What a marvelous tool!
I found the air screws needed to be 5 turns out on the front cyl and 5.25 turns on the rear cyl
the old lass now runs sweet as a nut! Thanx Doc!

Get a colortune - takes all the guesswork out of air screw settings - u should be able to find one on ebay for around £25
For replacement diaphragms and carb rebuild kits NRP Carbs in Manchester are the dogz danglers
http://www.nrp-carbs.co.uk/I also had trouble getting the carbs to synchronise
I found it was due to the roller on the throttle linkage being worn causing slack in the linkage so the throttles were opening out of synch
Of course, replacement rollers are no longer available - thanx Yamaha

However CMS in the Netherlands stock many discontinued parts including the roller at 6.50euro
http://www.cmsnl.com/products/roller_4x71426700/I found CMS after I'd engineered my own fix

I got a minature ball bearing - cost about £2, 16x8x5 I think it was from memory - best to check

The bearing wasn't quite as wide as the original roller so i shimmed it with a 8mm washer either side
A dab of bearing fit on the pin holds it in place
It works a treat!
I've finally got the rotten carbs to synch and get this - thanx to colortune NO popping and banging on the overrun!
lol life is good! :-D