Some of the transparency issues seem to be more complex than others, and are damn near impossible to repair with the texture patcher. I never figured out why, but I stumbled on some when i was updating it. Some I ended up having to 'fix' manually in Paint Shop Pro or GIMP. Dzarn also fixed all transparency/black splotch issues on Live (idk fully how), and the model files for any bugged model can be dragged from a Live client (and added to zones where needed since they are all individually packed now and not in Zone_chr files anymore) and it will fix the issue. But that would require you to have a Live client as P99 is obviously not going to redistribute those files themselves
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The best i can suggest is manual editing with a photo editor.