Since you have had the top end off as well that opens up a whle other raft of possibilities. As Geoff or Dave suggested are you sure the head is torqued down correctly and the tappets are set to the right clearance?
Also, did you have the head skimmed and/or what CR pistons did you fit? - is it possible the piston/s hasve touched the plug/s and closed the gaps right up.
Jetting can be complicated with velocity stacks, especially if you have the Norvil machined type but the jetting advice given in an earlier post seems a good starting point?
I seem also to recall someone else had a similar problem a while ago and that turned out to be a wire getting pinched under the seat?
Keep looking, you'll get there in the end!