Log SHIFTLAST, SPARKADV, and wideband...
then look at SHIFTLAST (does it match the shift time in the tune...?) and look at SPARKADV (what does it drop to...?)
usually the drop in spark advance does not cause the engine to bog (stock tune has a lot of TR and a long shift time)
also look at the wideband AFR/Lambda, what does it do during the shift...?
so basically I think it's due to fueling... $0.02.
post some log files
lol, we were all newbies at some time or other, and with all the new stuff coming we're still newbies