did you adjust the valves ? if you have a stuck valve it wont really run at all(on that cylinder)
and the 350 has a very short adjustment range on valve clearance a stuck valve would make it impossible to get an adjustment set
there is a specific range of rotation on the eccentric adjuster shaft that must be maintained
adjust the cam chain tension while you are at it
set the valves and do a compression test correctly on it, warmed up
there is no valve seals on a 350
piston blowby doesnt create backfires

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onnce you get the valves and static timing set set the timing for full advance with a strobe timing light it is the last and most important setting
put mufflers back onit and put the airbox back on you cant run straight pipes on the street,they wont work well anyway unless very long
besides straight pipes are for fucking assholes dont be that guy
and it is just as stupid to run stacks with no filters unless you never ride and just want to park it and look at it :-\
you need to see if you can get it to run stock before you fuck it all up anyway
if you cant tune it stock don't even bother trying with it all fucked up