What else can you tell us about the bike, (what pipes, what jets since you said the carb has been gone through already)?
I don't think those years have a crank position sensor like the 04'~06' or I would check that out as palemeat said.
If you pull out the choke/enrichner some can you ride the bike with minimal carb farts?
On my wifes 05' I took off the carb disassembled it and let it soak in a cleaning bucket for a couple of days. When I put it back together I bumped up the needle valve by one line. Then went through the air/fuel mixture setting and she doesn't fart once.
Get us the jet(s) size maybe they are to small.
95", 9.8:1 W/Heads by BigBoyz, 37G's, Arlen Ness A/C, PC USB, Supertrapp Supermeg 10-disc open cap