Here is my problem. I put a S&S super E carb on my 883. I run the smallest possible jets {060} The plugs are screaming eagle and are clean. Could it be timing? The bike backfires very, very bad. Please Help!

If your engine is backfiring through the carb, that is usually due to a lean condition. Backfiring out the exhaust is usually due to a rich condition.
Check with S&S about guidelines for initial jetting for your engine.
Be sure to tell them about any modifications done to the engine, exhaust, ignition, compression, etc.

What year sportster? Are you using a VOES switch?