Sam,
1. Have you, or your garage with or without your knowledge, ever put
K-seal (or similar) in the cooling system?
2. Don't assume that the vacuum filling has been done properly. Bleed the system yourself using the traditional method
here. Don't miss out any stages; follow every point exactly.
3. How do you know that the expansion cap is "sealing fine"? Is the system properly pressurising when at normal running temperature (as
murphyv310 has asked)?
4. Is the bottom radiator hose getting hot when the running temperature reaches the low nineties?
I think that your original symptoms pointed to a cooling system problem. It's never a good idea to start systematically replacing parts in the hope that you'll strike gold. This method makes subsequent diagnosis more difficult.
Don't change the engine. Start with the basics, don't make assumptions about parts being "fine", and work through the system methodically.
Simon