Once you have chucked the Zenor you can go your own way. Nothing else on the bike cares. If you do,make a sticker for anyone working on the bike that it is negative ground, under the seat is good.
The only other reason to stay positive earth is all those red wires, witch are really confusing when found on the negative side. So if you go, go all the way and change all the reds to blacks or Greens. Remedial color symbols help workers under duress.