If you pay him, you won't gain any goodwill, you'll just be donating to charity.

(He lives out of state, but has occupied the house in the past)  So all that being said, at what point does my persistence become an annoyance and potentially damaged my (remaining) goodwill with my neighbor? 

It's not a huge sum of money in the big picture (and is a reasonable amount to spend on movers and such), and it will build tremendous goodwill -- especially since you're displacing her and moving into the unit, she is more likely to leave it nice and clean and in good repair if she feels respected and treated nicely on the way out.

It was more emotional equity that built good will and helped the stick with us through the ins and outs of the 1031 escrow process.

This is not easy for out of area but I Believe its do-able with the right contacts in place, and big chunk of good will.

What I don't understand is what good will it do to include comps that indicate a 10%-15% higher value than my offer?

I️ am putting my own projects on hold to help this guy out but he is a good contact (he is in construction) and will help me with some other projects I️ have so it’s worth having the “goodwill” in the bank to help him out.

You might consider adding a line saying, "buyer's contribution to repair costs" if you want to have some goodwill with the seller, so that the repair costs aren't ALL s subtracted from your original offer.  

how good will that tenant be relative to him?

The agent who referred him either did so out of good will or is probably getting something out of it.