The problem with running game from steam may be related to steam client rolling back your files or godknowswhat, I won't be much help here, as I avoid Steam like a plague. Maybe Steam users know something about some client's option that checks file integrity or whatsnot?
As for Infinite gameplay - I know everyone have different game style, so it's not fun that some game limitation doesn't allow you to grind one sector endlessly. Although, if you're still happy to tackle on infinite, I would suggest proceeding straight to sector 3 (with a 2nd pass on earlier sector only, if you lack fuel for long-range jump), grind there for a 2 or three passes, then proceed to sector 6 and do the same. After that, you should be able to grind in sector 7 for as long as you want (or die, which is still possible even with fully upgraded ship and awesome equipment), before finally facing boss (or game crash after your 3246235432 pass through sector 7

).
In my experience, it works better than grinding sector 1 for ages - the stuff you get is just very low, there, and sector 3 is hardly more difficult than sector one (sector 4 have a quite step increase in foe's strength, same for 6 and 7, respectively). Not to mention that I find grinding sector 1/2 ultimately super-boring, but as said, everyone have own play style and sense of whats fun, so I don't want to play "uncle wise" here.
---
Sleeper - was/is the requirement to post mod load order in case of asking for help specified as requirement in 1st post, or I just imagined it? In the latter case, it might be worth to add it. Generally, helping anyone to troubleshot their problems without that info is quite pointless.
---
On a different note - I'm accumulating another list of bugs, stay tuned
Cheers,
/Estel