That is more or less my setup except with bridge ports except street ports. I had street ports before, then I tried bridge ports, and I decided to never go back 
(Although I did hear tell about a street port recipe that should be good for 270ish HP at only 7000rpm, might try it if I get enough round tuits) Also only two injectors for simplicity reasons. I guesstimated based off of reading things here there and elsewhere that the deadtime should be 1.2ms, for GSL-SE injectors running through a resistor block. I've got no good way of verifying that since all the easy ways involve an engine that idles smoothly.
My vacuum line from the ECU to the engine is a small diameter plastic line. Additionally, the line coming off of the non-carburetor's vacuum port has a hose coupler in it that has a section of spray can straw glued in place as a restrictor. MAP doesn't bounce hardly at all with this setup, nice and smooth.
When Autotune was giving me fits, it was after I had been driving for about 120-150 minutes. This was in steady state operation on the highway. I decided to try something I read online somewhere, just blandly tune the whole spectrum for 13:1, since the engine will idle, cruise, and run WOT at 13:1 just fine, then try leaning bits here and richening bits there as you find suitable. Which is why I decided to play with "incorporate AFR table" mode, so I could make the AFR table all 13s at first, and then enrichen/enlean THAT table instead of mucking about with the VE table. I pulled off the road, made certain cruise ranges 14:1, and autotune was adding more and more fuel there, when it should have left it alone since that area WAS more or less correct. Annoyed me to no end.
I also think the 680cc injectors might have been sticking open from sitting so long (3 years?). My initial tune that I SWAGed together was running so horribly rich that the engine was sputtering and blowing clouds of blue smoke, and the WOT VE figures were in the 90-100 range. And autotune won't work if it's misfiring, you go into a positive feedback loop of adding fuel and misfiring harder. It ran cleanly at 3000 (where the figure was like 80) and my torque curve is pretty flat, so I just copy/pasted the 3000rpm column all the way out. And sure enough it did pull cleanly there.
My final-ish tuning tables after 500 miles of driving (still slightly rich over 8000 but not disastrously so, like 11.5:1 on a 12.5:1 target) has the VE figures... in the 90-100 range.
So, I dunno. It's quite happy now although I still need to do some work in the low MAP/low RPM region, which is tricky because the engine never runs there except when coasting. But you know something's not right there because there's a hiccup when reaccelerating, or if you upshift slowly. (I usually drive so that I keep the engine in the 90kpa range and upshift at 2000rpm or so so that I can accelerate as slowly as traffic does) Everything under 60kpa and 2400rpm is a total guess, it idles at 75-80kpa.
