It's been long enough, I'd say it's fair to do the maps. Having submitted a few maps but not following through with more doesn't exactly retain "dibs", certainly not over a few years.
Though I think it would probably be better to redo them from scratch than to add to an existing map if you can't get their permission.
If the original mapper did perfectly (or exactly how you would have done it) with what they had already assembled, and that the end result is the same, one could argue that it would be a waste of time to do the work again just to be "above reproach". I personally think that I would still do it though, if it were me.
(Though funnily enough, this very morning I had a brief moment where I mused about redoing all of the A Link To The Past maps (while I did the Light World, Iron Knuckle did the dungeons and Alex Foster did the Dark World), in a sense, to try to "claim" one of my favourite games of all time as mapped entirely by me, I also realized that (besides not having made a map myself in years), I probably don't have the time, and for so little gain.)
Looking forward to The Legend Of The Mystical Ninja maps. I really like the Super NES game. It's one of those games that may not be supremely well-known, but is still a high-quality game (comparable to the "AAA"s, even if not by popularity) and is of a decent length and lots of fun. Could also say the same about the first N64 game (I didn't play much of the second). A shame that Konami didn't bring more of its games over, but the Goemon series is full of Japanese quirkiness that makes it hard to sell, even though that's a big part of its charm, IMO.