Either make the holes before cutting out the blocks or make the jig to hold the block.
My shelf pin jig makes holes about 4" apart about 2" from the edge of the board, so it wouldn't work for your application. You could certainly make a router jig for your needs though.
Mine is a small plunge router. There are a number of them on the market that should work. Make sure that you can get the bit you need before getting too invested in this idea.