Of course, ultimately, it's your decision but let me just throw my 2 cents into the hat...
I purchased a 1988 K5 that was supposed to be 100% stock and mechanically, it is. That's what I wanted because I didn't want something "cobbled" up by some PO. (It ended up being cobbled up in the interior department anyway.) Bought off internet sight unseen...I'll never do that again!
Anyway, I mulled over a set of aftermarket vortec heads, headers, dual exhaust, cam, carb, etc. Then I added it all up and realized I wasn't going to expect a race car out of a truck so I just decided to keep it as is until the engine is totally worn out THEN decide if I want to put all that stuff in it when it needs rebuilt. In the meantime if I decide to sell it I'll get more from it in stock form. The resell value, by my calculations, would go down about the same amount that I would spend on the parts so I'd probably lose twice what I invested...could be right, could be wrong.
Upside is, either way, if you do the upgrades correctly you'll know they were done right and you'll know exactly what was done.
One thought, if you don't address the rust issue it won't matter since the worse it gets the more likely you won't be as happy driving it around anyway, IMO.