Between the 4cyl and V6, these cars came out with a number of different configurations of tailshaft, and when you buy a car as a group of parts like you did, you never really know if they all came from that particular shell. I'm not saying this is the case, but it could be possible the tailshaft is from another small ford.
If you look at the following reference (and cross-reference) you can see that Capri uni joint caps got as large as 25.4 mm diameter, but if you look further down on the Hardy Spicer catalogue you'll see a different uni joint for T series Cortina 6cyl (RUJ-2038R). These have a cap diameter of 27.39 mm.
http://www.hardyspicer.com.au/PDF_Fi...15lr.pdf#page6
http://www.viclube.com.au/public/upl...MAY%202011.pdf
It may not be the reason you're having issues, but I just wanted to suggest the possibility before you spend too much money trying different solutions.
Cheers
Jamie