Ok so apparently I
hadn't actually broken any pins at all, just bent them. Only thing broken was the middle divider which I just epoxied back to it's place and did some bending for the pins and now the USB 2.0 ports seem to work fine again. The one on the right side was in a lot worse shape and it's still not 100 % good as new but let's see if it'll give any issues in practice. Weirdly it seems to temporarily disconnect if I push the plug too hard inside but if there's no pressure then the connection seems secure. Also not sure how much the pins like bending back and forth and how long they will end up lasting eventually but we'll see.
But as I was already set on upgrading the front panel to this decade and the assembly plastic turned out to be surprisingly soft and quite easy to cut with a knife (I had assumed it would be some hard ABS), I decided to do a surgery and remove the FireWire port with the intention to replace it with USB 3.0 while keeping the assembly intact on one side to be able to still secure everything to the case as earlier. Firewire at least wasn't on any PCB, just the cable going through the assembly and hotglued in place. If I had known that I could've just removed enough of hot glue and pull it out but I was expecting to have to solder it off the presumably common PCB with the USB ports so I removed the cover from one side altogether.
On the motherboard there's two USB 3 headers: one 19 pin IDC20 header and one Type E / Key A USB C header (only Gen 1 unfortunately). Ideally I'd like to utilise the latter one and put a type C connector then in place of the FireWire port since I think it should fit nicely (=without cutting) the existing holes in the case. USB A is a tad too tall and I'd like to save the 19 pin connector as I've been planning to get a 3,5"/5,25" card reader (to get rid of the one on the desk) and those typically seem to utilise the 19 pin connector. Also, I was planning to put just one USB3 port there so it feels like I'm "wasting" the other supported by the same header.
I tried to find a simple Type E / Female USB C cable and the best option I've found so far is
this cable by Fractal Design that is designed for it's Pop / Focus 2 cases but seems to be one of the rare cables with the connectors I'm looking for. I'd probably need to trim attachments on the C connectors to make it sit on the front panel assembly but assuming it's similar soft-ish plastic then that shouldn't be an issue. More of an issue seems to be that it's not in stock in the nearby stores at least. If I can't find a proper USB C cable then I'll probably end up going with a single type A connector cable.