[Rory McNeil]

Ford used 2 different fuel pump eccentrics on the 63 1/2 and newer FEs, the older engines used a thick 1 piece eccentric, which used a long dowel pin in the cam. The pin should stick close to flush in the eccentric, the cam bolt washer holds it in place. Later FEs (not sure exactly when), used a 2 piece eccentric, with one thin inner piece, with a slightly larger outer ring that slips over the inner. (I am guessing it was a friction reducing modification). With the 2 piece eccentric, a shorter dowel pin is used, as the inner eccentric has a small tab that fits into the dowel hole of the cam gear, so the pin needs to be short enough to allow this tab to fit inside the hole, and allow the inner eccentric to sit flush against the cam gear. `The cam dowel hole in the camshaft does not go all the way thru, so if there is something jammed in there, you wont be able to push it farther in, assuming it is bottomed out. I suppose you could shorten the pin you have, but i would be concerned if .325 is a safe enough depth for the pin to fit inside the cam.
Also, if the old timing set was origional, the backside of the cam gear is flat, with the thick C shaped washer that is a spacer, that fits inside the cam retainer thrust plate. Every aftermarket cam gear I have ever seen has a built in step on the backside, so DO NOT reinstall the C washer. To do so would cause the cam gear to not be parallel with the crank gear.
As for your timing marks being off, are you using an ATI Damper. I have had a couple of these that were off by 7 or 8 degrees with the OE timing pointer. If it is a OE Ford balancer, there is a possibility that the outer ring has slipped on the hub. do you have another balancer you can compare with.