I didn't know there was so much problems getting both the Restoration and the Refit hacks to work right together, they use to work somewhat alright when you combine them back then, I'm guessing the latest version of Refit changed some things that makes it incompatible with mine.
I updated the description in my hack alerting everyone that it's not compatible with Refit anymore. Sorry everyone, I didn't know.
The only thing I can think of is make a alternate patch for Restoration that will add the shorter charge time and the increased invulnerability from Refit.
That might be the better option, because I was thinking of getting help on re-localizing the script to be closer to the one from the Japanese version like the other users on here did with the SNES MMX games.
The two patches do work correctly together, nothing game-breaking occurs. The only problem is that both patches try to update some of the same lines of text, so those lines appear garbled. The description of Rush Jet in Auto's shop is also broken. I compared the two roms in a hex editor, compared against vanilla MM7 to check. Refit rewrites a number of lines of text, because part of its custom font includes a new character for "r.", so all instances of "DR. WILY" and "DR. LIGHT" are replaced with "Dr.WILY" and "Dr.LIGHT" with no spaces, and a single character "r.". That led to some of the issues, like "Dr.WILLYY". Also, Refit replaces the item descriptions in Auto's shop with more descriptive ones.
For my personal use and curiosity, it was relatively easy to create a combined rom of both hacks, including the new title screen, without any of the text issues. I patched with Refit, removed the custom fonts and graphics (using the graphic compression/decompression tool to swap in vanilla MM7 graphics overtop of Refit), fixed/reverted the text issues with a hex editor using a vanilla MM7 rom as reference (leaving the item shop changes), then patched with Restoration, and repeated the process for any remaining text issues. I also changed two lines that always bothered me ("You better tell me who you are?" to "You better tell me who you are!", and "I gonna do what I should've done years ago" to "I'm gonna do what I should've done years ago").