I had a similar issue with my FI set up at first, it took a while to figure out what was wrong. Everytime I started the engine everything was reset back to new, or how it came. The computer was erasing everything it learned each time the engine was shut off, the problem was that I had everything under the main shutoff switch and the FI system requires a constant 12 volts to retain memory. After about 2-3 runs it finally settled down and started running great.
Not sure what set up you have, but I think the Mass Flow is only good up to so much horsepower, I know your engine should be atleast 500, and you may be running out of fuel... just a thought
I used the Power-Jection III, and its rated for up to 550 rwhp, my engine dynoed just over that in a mustang. At wot it will lean out just a lil but not enough to cause issues. Try a fuel pressure gauge and see what it shows when it starts to act up.