MR-1 reactor and bio-pellets

I finally got around to installing the MR-1 reactor (modded with the needlepoint mesh) and got it started. First time out, the pellets only tumbled on the sides with the two holes. I took it all out and drilled two more holes, slightly smaller, and I still get tumbling on only two sides. I suppose I should have made the holes the same size. Seems stupid now not to have done that. Do I have to tear it all out again and do that, or do you think some movement in the reactor will suffice? 
For those of you who might have done this same mod how did you treat the holes under the bottom plate? I've read that some have replaced it with a 3/4 slip fitting drilled full of holes. That wouldn't seem a hard job, but if I don't have to do it, I don't enjoy this sort of tinkering.
Thanks for any information you might offer here.