Welcome to the site and congrats on the new bird. Some photos would help, I think, as you're describing some unusual issues.
The canister fuel pump is correct and should fit. Either you've got the wrong part (perhaps one for a truck application) or there's something out of kilter with the suspension causing the interference. You might try comparing the dimensions of the pump with those sold at a dedicated tbird part dealer, like
Bird Nest | West Linn OR | 1958-66 Thunderbird Parts
The smog pump was a California-only item, so pretty rare. I have a 64, so didn't have to deal with it. Others have, though:
https://www.vintagethunderbirdclub.n...og+pump#p97800
~Steve