What your experiencing is what I call inline shock. Chevy sixes are just expensive to rebuild and especially the older 216-235's. The cranks have shims and are sort of tapered from end to end and I think that scares a lot of rebuilders or at least provides an excuse for high charges. The parts are expensive too as compared to a SBC for example.
I'd suggest you pull the rod caps and have look at the journals. If they seem good then chances are the mains are too. You certainly can hone the cylinder walls yourself with the aid of a Shop Manual which should be your first purchase. If you replace the cm then do the lifters and gear also.
Sounds like your fairly handy so go for it. You can do it as thousands of others have. Lots of experts here (not me) to help you out of a spot. Incidentally...$3K sounds high to me too but repair costs are regional. Is that for ALL new parts and labor?
