This is all good information. I assume grancuda would like to keep as many parts as possible that he already has.

The options I see are:
1. cut the nut a little like 4406bbl mentions.
2. replace the compressor bolt with an allen head (rounded/flat head) & run it the other direction through the compressor so the nut is on the other side. This may make some compressor seals leak?
3. find a thinner thermostat housing... I do think the stock ones (at least on big blocks) are "stepped" in that area. I like this idea best if it's possible.
4. Grind a little clearance off the thermostat housing.

For the heater hose outlet....can you find a 45-degree outlet & use a bunch of Teflon tape so that when it's tight, it points away from the compressor? You might have to try a few times to get the right amount of Teflon tape OR maybe use some "reactive Teflon paste" so it will still seal even if it isn't 100% tightened?