First off, have you looked around inside the block to see if there is anything in there to even worry about? a light patina of rust isn't going to be any real problem. The shop should have at least hot tanked it before machining. If fact, they would have needed to clean it just to magniflux it properly. You did have it magnifluxed, right?
Since you have had it machined allready, I would just visually inspect it for crusty gunk, especially the rear 2 cylinders, and let it go at that. Trying to flush it out with costic chemicals now could cause more problems than its worth. If it is full of crap, I would take it back to the shop and make them deal with it.
As for chemical rust removers, I have used a product called Oxisolve. Eastwood sells it, and I usually see dealers selling it at the larger swapmeets around here. It won't do anything to the gunk inside, but it will remove any oxidation to metal parts.
