A hack that adds Timeman, Oilman and Bondman would be my dream hack too! As far as keeping things compatible with this version, the only changes the patch makes by default is the changes to various tiles which are otherwise identical to other tiles (this is so the HD pack can pick up and support those tiles) and a few minor level edits, I think in Fireman's stage mainly. Then there's the music patch and the pause patch. Otherwise, it's just plain old MM1.
If you wanted to build off the most "necessary" changes, use the Pause Intact NES music patch so all the graphics and level tile edits will work right out of the box. However, some of the tile edits I made were quick and dirty since I didn't need to care what vanilla graphics look like so long as the tiles were not duplicates. You'd probably need to revert some of the changes later to make a non-HD Pack release that doesn't look messy in spots.
Might be easier to just build off a vanilla ROM, it wouldn't take much for me to re-implement the modified graphics and and level edits afterwards.