Rusty,
1. Have you been running the engine without a prop?  If not, I don't think
you will get dependable readings or adjustments.
2.  The EC2 is set to stage the secondary injectors at 15" of MAP, so John's
staging theory is probably correct.  I would not worry about this low rpm
stoppage for now.
3.  Tracy's specs for timing (with the static timing set of 35*BTC) are:
1500-2499= 10.625*BTC, 2500-3599=18.5*BTC, and >3600= 21.875BTC.  Also, low
MAP(<22")  will advance 5.625* when above 3600r.  If it were me, I'd reset
the static set up and check timing at 3500-4000.
4.  Glad you found the miswire...
Tommy<><