I say go for it. You can't buy a 1st gen 4runner for investment value like you would a classic muscle car or an exotic sports car because you have a realitively small pool of potential buyers. In this economy, the muscle cars and sports cars aren't even a sound investment anymore.
Even if you had an ultra-low mileage 1985 loaded SR5 4runner, and let's say you were going to ask 12K for it. Sure, everyone on here and Yotatech would be drooling over it (I would too!), but how many on here would have that much money to buy it? And then we'd face the same mod dilemma you have.
When I bought my 85, it was a solid platform but needed alot to get it to where I wanted it. But honestly I could have gone for a factory fresh restoration if I wanted (even though it had passed 300K) or I could semi-restore it and mod it how I wanted in the process. I went with the latter. They way I look at it, I have as good a chance finding that "right buyer" for a modded rig as I would for a stock rig if I ever go to sell it.
IMO- Do what makes you happy, enjoy your baby and never look back. The mod bug is all powerful!