Also, if you leave the amp stock, you should be able to get more money for it when you go to sell. The only exception would be if you had Pass do the mods, instead of going after market.
Not true, any Threshold amp refurbished by Jon Soderberg will be worth more, however not nearly as much as the cost to refurbish. Just to make sure you know, Jon worked for Nelson Pass at Threshold as service manager. If you asked Pass, it wouldn't surprise me that he might refer you to Jon Soderberg.
If you like the sound of the amp the upgrade sounds like a good deal principally because you'll have refurbished all the parts that can go bad (I don't know about the sound quality difference). Just realize that you're not getting your money back from the upgrades, just musical enjoyment. That may well be worth the investment.
Agree, having the work done will improve the sound, but how much might be that $64,000 question. Keep in mind that any old amp will need to be serviced for reliability, and if there were any old amp I'd spend money on for service, it would be a Threshold.