Theres a program called Smart Cutter (not freeware unfortunately) that allows you to precisely cut h264 streams and only re-encodes the frames around the cuts, so it wouldn't be necessary to have a fast PC if the censored parts are the only parts you'll be editing.

I was also thinking about taking the uncensored scenes from the HD Remaster DVD and adding them to the BD, but it would probably take me a long time to get around to it. First I wanted to make a custom Japanese subtitle file made from the original script and some transcripts I found online, but I'm not even halfway done, then I wanted to re-translate some parts of the English fansub script since it has some errors IIRC. I'll also be synching the audio from the PILA-7008 LD and maybe the "theatrical audio" from the 2nd disc in the HD Remaster DVD box.