1. If you had asked someone they would have told you that he had been there for years and left/would have left (leave) it at that.
Is there a need to repeat the "would have"?
2. It was surprising that no one noticed his absence. But one morning he just wasn't there. In the village post-office, the center of local gossip, he hadn't been missed/wasn't missed (not miss) for several days.
My professor first said it was "wasn't missed", then he wasn't really sure what is correct, but doesn't "for several days" require perfect tense?
3. Tom was gone, there was no doubting that. Every possible place he could have been had been searched/was searched (search) without finding a trace.
I'm not really sure about this one, my professor said it was "was searched", but thought what I wrote wasn't incorrect and kind of left it at that.
4. There was no sign of disturbance. Everything was just as it should have been/should be (modal+be).
5. The only thing different was that he no longer spent his evenings in the pub as he did/had done (do) before.
Again I'm not sure, but I didn't use the Past Perfect because I didn't think it's used to express routine (and I checked my grammar book, it doesn't say anything about using it for repeated actions). Also, there's the "before" which makes the time pretty obvious.