you can also get an internal 3.5" bay hub, they come in 4+ port varieties, these have a usb cable attached, you'd have to route the cable back to your external ports.
you cant simply solder ports to the existing pinouts cuz that would confuse the controller. what is on the motherboard is a singular controller and a root hub which splits it into 2 ports. any hub you get is an intelligent "splitter" so it's not a matter of just adding more ports. you need a control chip to actively switch\separate signals to\from devices and the controller. it's the same basic concept of a 3 device IDE cable, it just doesnt work that way.
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i apologize for the previous reply, i will leave it as it is though. I miss understood your intent.
as for that pci hub thing, it's not really a pci hub, it just mounts to the expansion slot cover, there are no parts of the pcb that actually inserts itself into a slot. since you dont want to waste a pci slot, you can just waste the ISA slot that's there. OR you can do a little modding to the expansion slot cover that the hub is attached to, and mod your case, and have that hub mounted to a part of your case with rectangular holes for the actual use of the ports.