Going back,
I have looked and there does not seem to be room to manoeuvre on the bottom pulley.
The crank dimensions have generally been (in relation to this problem) the same since 1939
The bottom gear (6306) has had a 48 prefix across all models (it seems) of all relevant Ford V8s up until the reverse cut gear of the 8BA, (in the fifties)
So, to me it's like this:
Front of crank, the gear goes on, the slinger goes on, timing cover on,the pulley slides home.
There's not much you can get wrong in that.(is there?)
I'd like to know why the sheaves of the Lynx are set out further than a std pulley. Of course there will be a reason, but I can't figure it out.
I have a motor with the same timing cover. It has a std two sheave pulley on it.
Is it about the belts clearing that Dizzy box?
Anyhow it seems the answer lies in the pulleys and pumps as deduced.
To add to Mike's effort, the 78C number prefix refers to the bush type (single sheave) pumps and the 79C, refers to the twin sheave bearing pump housings.
For H.Ford to come up with a different part number (C29SR- 8505 and 8506) means those housings were special. Theat may not mean that they wont fit, It might be say, just a better water flow (if you are lucky

)
Maybe David H. has hit on the answer? ... and it can be fixed with T16 pulleys? (remember though the part that changed was the housing)