Wow, that's cool, so you replaced each of the game's functions individually until you had the majority replaced and working stand-alone?
Can the assets be "reverse engineered" as well?
Also, can R* shut this project down? Is there a legal basis for them?
Of course, R*/Take-Two could always make a case.
That would be copyright infringement. At that point, you might as well just hit copy files from the original game.
As for the legality of the whole project: there's several different legal objections one could raise under copyright law:
1. That the EULA prohibits reverse-engineering
2. That the resulting reverse-engineering project is infringing the copyright on GTA3's program code (which it kind of has to in order to be a faithful disassembly)