After shuffling load order, I can see the PEG container seaport (and other PEG ports) again, but SC4 is now complaining about 3 of the BSC ports missing. It says there are "missing plugin packs" even though the packs are right there.
So I now suspect that the PEG enablers made for 3.0 are no longer quite right for 3.1. I guess I'll have to dig into the editing and figure out how to change the IIDs a little bit more so they land in still-unused custom port slots.