First off, let me say your V1.9.8 is wonderful and very well thought off. I did run into two things, I don't know if they are bugs or not, but I thought it would be worth mentioning:
1. After editing and maxing out the stats of a male and female normal chocobo caught(not created) and after getting them up to s class in normal racing, I noticed the normal nuts for getting river or mountain chocobo's (carob nuts) only produce regular chocobo's after 30 tries. While I also tried it with created and modified chocobo's as well, same results. I don't know if it's a bug or not, or the randomness generator always denying, but I thought it was worth a mention, as it might apply to higher level chocobo's too.
2. when I was working on getting materia set up so I could go after the weapons, and I was all set, I looked at cloud, and saw he had 10 MP? I checked his status, it was 10 out of 10 mp. I tested every materia, and tracked it down to the Individual green and red materia. When equipped, created at master level, first level, it does not matter, it knocks you down to 10 out of 10 mp. If you use the blue materia combo's like for example final attack-revive it will cast life 2, but because you only have 10 mp, it will not work, and you die. I tested it with new materia after the previous one gets mastered, and ones bought at stores, same results. While I am no expert, and I hope it's not in the steam version of FF7, but if it is a bug in 1.9.8, I thought you should know.