Now that DP2 has been installed, you'll need to either reinstall BOE v2, the fix, and the DP2 fix - or, just the standalone. Either of those solutions is okay.
To quickly answer some other things (without quoting, I'm on my phone and it's being finicky)...
Bayern Munich are fine for me, including Ribery being present. I'm not sure if the instructions aren't as clear as they should be, or, if it's because I had v2 and the v2 fix installed pre-update (but that shouldn't be necessary in theory, as long as they're installed post-update).
Also, there are a handful of fake players that appear in the ML but unfortunately they don't appear in the edit mode - they stick out because they've got blatantly jibberish names like E. Castledine (and worse, but I can't remember off the top of my head). So there's not much to be done there.
Thanks for downloading, guys - and extra special thanks to those who've donated, especially in the last 24 hours. Truly touched by the generosity of this community. If only Konami were so generous (in the form of not screwing up our hard work)...!