Backfiring and cold natured '89 Suzuki 750 Intruder?

Hello, did you jet the carbs to match the pipes? This could explain the hard starting and the backfiring. Aftermarket exhausts are usually free flowing which will lean the mixture. A lean mixture will definately cause it to start harder. Also a less restrictive exhaust can actually cause a vacuum in the pipes, resulting in a small amount of raw fuel being pulled into the pipes resulting in a backfire. Definately be certain you have the right temp range plugs, and a well charged battery for the cold starting. Does the engine also surge a bit with a constant throttle position? This is also a symptom of a lean condition. If available I'd run this bike on a dyno, there's a shop near me that'll give you 2 pulls for $25 with a tuning session inbetween, WELL worth the money in what you'll learn from it. I know you said the carbs were cleaned 3 times, but were the float levels checked, have they been synced, what sort of airbox and filter are you running? These are all little things that can cause problems. I'm sorry if this doesn't give you an instant answer but I hope it may have given you a few ideas and pointed you in the right direction.