The shop that did the machining on my block had a machine that registered off the center line of the mains and cam. If they were machining the decks they couldn't help but square them with that machine. This same machine was used for the ruff boring prior to the finish hone with deck plates.
It cost me just shy of $1050 to have the block cleaned, magnafluxed for cracks, the cylinder walls sonic checked for thickness, the mains checked for alignment (didn't need to be machined), bored, decked, finished honed with deck plates, new cam bearings installed and painted. This cost also included balancing the rotating assembly which needs to be done with the KB107's because they are so much lighter than stock. I had had the crank cleaned, magnafluxed, turned 0.010/0.010 under and polished prior to bringing in the block which was $250.
If you do not have the money to do it right it would be more appropriate to just rering and regasket the engine and run it until you have the money to do it right.