I'm not a master motorcycle mechanic by any means, but process of elimination is the way to go. An engine needs compression, spark, and fuel to run. You have compression, so I would start with:
Eliminate spark as an issue.
Gap Plugs
Spark Test (take plug out touch against cylinder head and check for strong spark)
If you are having spark issues then it is an electronic problem, or a short somewhere on the plug lead.
Check spark plug leads for worn or bare spots that could cause a short to the frame or cylinder head (I had this happen to me on a boat outboard once, temporarily fixed with a good wrap of electrical tape on the bare spot, but get new leads!)
You can swap the leads on the cylinders to see if the problem switches over to the other side.
Use a multi meter to check plug leads for breaks in the wire
or just replace them if they are old and worn.
Still have spark problems? then look at your CDI
If you have strong spark, it's probably a fuel issue:
check for vacuum leaks
clean carbs
sync carbs
check valves for correct operation and clearance (you should do this anyway)
As for your exhaust, there is always a good chance that a previous owner did not know to re-jet the carbs after an exhaust change. I'm not sure what is required for the MAC 2-1 but there is a good chance it needs to be done. It is unlikely that would cause your one cylinder problem though. But if you are seeing hesitation throughout the throttle range after everything else is looked after, then re-jetting/carb adjustment would probably help. 400 twins are apparently famous for being tough to re-jet and run smoothly after air-filter/exhaust changes.
I am sure other more experienced mechanics can chime in to cover what I have left out.
Andrew