I'm using ... FuSoYa's VWF and Vifify93's Proper-caser patches as a base.
Since that is how I play the game, with those 2 patches, that is a very good base to start out with, I agree 100% with that decision. Very smart, you start out with a variable-width font and everything in the correct case, but without any hacks that change things from the way the game originally was designed.
Your idea sounds pretty good. I would refer you to this unfinished project attempting a retranslation: http://www.romhacking.net/forum/index.php?topic=19920.0
Some of the people who worked on that project might the text of their unfinished retranslation or some tools to recommend that they used, and they might be able to help you out. Apparently RedScorpion and Thanatos-Zero worked on this. Also Hiei- worked on it too but it seems his/her work was separate and not really coordinated with RedScorpion and Thanatos-Zero, from that thread. It seems RedScorpion and Thanatos-Zero never finished their project but Hiei- DID pretty much finish an English translation but never put it out because Hiei-’s work got dismissed by Thanatos-Zero because Thanatos-Zero and RedScorpion were doing their own translation, look at http://www.romhacking.net/forum/index.php?topic=19920.msg285004#msg285004
as well as the comment immediately following it.
My point is that Hiei- already retranslated this entire game but it kinda got discarded since it was submitted to another project that didn’t really accept it and was trying to do things differently, but you could totally use Hiei-’s work, Hiei-’s profile is here: http://www.romhacking.net/community/1586/
Maybe Hiei- still has their translation of this on their computer. My point with mentioning this is, after I discovered this while reading through the forums, I thought, well, this unreleased retranslation would be very very useful especially since its creator says it is 100% complete. Too bad it never got released as a patch.
You aren’t actually planning on doing a retranslation from what you said, only uncensoring and updating and relocalizing it, but, Hiei-’s unreleased work translates everything including the parts that were censored or left out of Ted Woolsey’s version, so if you are reinserting those parts it would come in handy.
As far as names I think generally the 3D Remake versions released earlier in 2018 for PS4, PS Vita, and MS Windows of Secret of Mana would generally have the best names for most things although I agree, you might want to keep older names for other things, I trust your judgment on this. You don’t really need a copy of the game to find names of things, you can find things like lists of weapons, armor, accessories, characters, game locations, etc. online and see what has changed between the SNES release in English and the 3D Remake in English.
EDITED: There is a Secret of Mana Editor by Moppy you can use. I updated Romhacking dot net’s version, at http://www.romhacking.net/utilities/985/
, from the outdated version 0204 to the latest version 0213 that is at its official site, http://somedit.blogspot.com/
, so now, either site you get it from, you get the latest version. Anyway this editor may be helpful to you although from what I have read it does still have some bugs and is not entirely perfect so I would be careful with it. (Originally I posted this before Romhacking.net had the latest version approved, I edited it now that everything is up-to-date.)