UPDATE:
The dreaded shudder is finally gone!
I had a chance to replace my spark plugs, and the problem just went away.
The car idles more smoothly now too.
Strange thing is that though the plugs were a bit overdue for a change (40K miles vs recommended change at 30K) they were in very bad shape.
Could this be due to the MAF sensor problem that was recently fixed, or is it an indication of something else I should look into?
Dapatch - when were your plugs last replaced?