if you have issues with vacume, id lean towards mechanical timing/boost leak. i had issues like this for a while with a build i did a few years ago, and was ripping my hair out. it was suggested to me to go back and check, i got all sorts of indignant about it.....long story short, it was off, somehow i didnt set the tensioner right, even though id put doxens of sr's together. check, so you can right it off.....it did exactly what your describing. if you really have swapped ecus around, and dont notice a difference, id have to say look elsewhere for answers. if you really want to check, put a stock ecu, injectors, ad maf combo on it just to see if it will idle/rev.....but anyways.