OK, so I have a question - is your MegaQuilter the smaller one (like a regular sewing machine) or is it the mid-arm (18inch) machine? I have the 18 inch one, so if you want to tag me off-list, you can.
Other than that, here's my thoughts...
First of all, I wouldn't worry about using the larger needles - once the quilt is washed, those holes will close up. Also, even without washing, eventually the fabric will "relax" enough that those holes won't show. So, using a larger needle could help.
Secondly, is the top thread just breaking, or is it "shredding"? If it's breaking, you may still need to tweak the tension just slightly, if shredding, check the throat plate for any burrs or even check the needle.
And lastly, it could also be the thread weight. I've had issues with the heavier weight threads off and on, I find that my best success is with 50wt or 40wt threads. Anything heavier and I have major issues with tension consistency... it will be too tight on top for awhile, then too loose for awhile, without me even TOUCHING the tension. And it COULD be that particular spool of thread!! Just like with automobiles, you would think that they're all the same, but every once in awhile, you find a lemon. Same with spools of thread. I had to toss a pretty large spool myself (I gave it to someone who hand-quilts) because it just did NOT like my machine.
Hope this helps...