Quite a few things wrong with that Tune. No wonder you are having issues with AE. Made some revisions to.
1: AE settings. No where near correct. Made several changes there that should be positive.
2: Target AFR table far too lean at low RPM. VE table greatly affects transition off idle. Going too lean creates a bog. With proper Ve Table, less AE is required.
3: You were running Alpha N. MS3 has a special Fuel algorithm for ITB's. I have enabled that.
4: Spark Table needed some work
5: I've noticed that you have your O2 feedback control disabled. I have enabled it but set proper settings and filters on it.
Send me a PM with your E-mail address and I will send you a touched up Tune. This is just a Baseline . but should be an improvement. I also do Remote Tuning and offer full Tunes built for your particular engine specs.