...[Igniters can be eliminated since I swapped connectors and checked the signal, the oddities move with the connectors!]...
This is interesting...I assume that you switched both ends of the connectors...between the igniters and the coils...so that you did not produce a misfire. I don't know if a difference in the output of the coils is normal or not.
If the wierd signals moved with the connectors, that would point to the connectors...right? Have you checked continuity? connector condition? broken or partially grounded wire?
Also, since your problems seem to relate to throttle position, have you checked or adjusted your TPS???
Did you have it off the throttle body when you cleaned it?? How are the connections?? Check for continuity on the idle contact and a smooth linear change in resistance reading throughout the full stroke on the throttle position pot.
If it checks OK, it wouldn't hurt to adjust it a little. I read in another thread that an out-of-synch TPS caused rough running.
There is an adjustment procedure on the lexls.com site.