Sounds like you need new plugs! Change those plugs with stock ones. From spark plug condition, it sounds like you were running lean.
http://www.rmh-d.com/service/spark_plugs.php When you do a upgrade like that, the PCIII should be the first thing you get. The pipes are without question the coolest outward part of your upgrade, but dealing with your fuel is top technical priority.
That Twin Cam 88 is well engineered I'm sure you didn't hurt it. Change those plugs ASAP and be sure you get the right map. For big shot longs PCIII gives you 2 options; with or without baffles (M805-177).
For my Dyna, I'm making the assumption that the Arlen Ness Big sucker is close enough to the SE air filter, but eventually I'll get my scooter to a dynamometer to finalize my PCIII map.
http://en.wikipedia.org/wiki/Dynamometer