Vibration may mean the harmonic balance has gone south. Check to see if there is any rubber protruding from the HB on the engine side and/or a wobble.
Your best bet for plugs are copper core style. You didn't say what plugs you used. Recheck the plug wiring to make sure they are all seated and in the correct order.
I do suspect you may have more than one issue.
Before spending a ton of money chasing hunches buy a OBDI code reader for about $22.00. You really need to be able to see what the computer is sensing to properly diagnose electrical issues.
KB 2.1L, FRPP M5400-A Suspension System, FRPP Aluminum D/S, Shift Kit, Built TC, FRPP 3.73 Gears, Balanced Roller Cammed Engine, Edelbrock Performer Heads, Comp 270AH cam, AEM EMS, 3.5 Bar MAP, Zeitronix ZT-2 WB, FRPP 70mm TB, hardened AODE, modified UPR CAI, Be Cool Aluminum Rad