Homer wrote:
I wondered at the time if any additional components had been left off the motherboard during manufacture.
Nope, there are no parts apart from the header itself.
Personally, I wouldn`t remove the old pins, just trim them down to avoid shorting on any clockport card, as it`s not worth the risk of lifting a solder pad.
BTW, if the original poster was having trouble getting a new header, RS components have them,just look for 2mm IDC headers.