Missing under boost?

[batmanfc]

Just got my motor put in. The car runs ok. I believe it still has a vac leak I haven't fixed yet but I don't think it is causing this. Whenever it gets into boost it misses bad. Pulls the best in first and second gear but still misses some. 3rd 4th and 5th are horrible especially up hill it almost dies. In 3rd 4th and 5th the miss isn't nearly as bad if its not under boost and it seems to have a little more power out of boost. Kind of thought that may be a MAF going bad? Also when under boost you can hear a noise that almost sounds like a pebble bouncing around in the intake. Its not real loud but noticable. It idles on its own but fluctuates between 750 rpm and 1000 rpm. It also takes it a few trys to crank. It will crank everytime you try but won't run and hold idle until the about the 3rd try sometimes a few more. Not exctly sure what it is. Thought I would ask and see and listed all these problems to see if it may all come back to one thing. I may still have a few vac leaks that I have to fix too. Don't know if that would cause all of that?