I just took a quick look at your main VE table and it has a lot of peaks and valleys. I would work on smoothing that out. For example, your 1200rpm line goes 51-55-50-57. Also your 100KPa line has a dip between 2000-2800. Your 40 and 50 KPa lines both have dips as RPM increases. Your PE table is set at 12.7, so the ECU is doing what you have that set for. I'd maybe try disabling PE so you can focus on the main VE table without the PE effects. Remember anything above 3200rpm is going to use the 3200rpm cells. PE is kicking in at 48% of TPS - what is your TPS reading at 4800rpm and mid-load? After you get the VE smoothed out you might want to look at when PE comes on.

Just my 2 cents. YMMV