I'd check over on DiscoWeb, since these are their specialty. I have never seen or worked on a Secondary Air engine, so I'm not sure of the differences. But, if I were changing out an engine, I'd go for a 4.6L instead of a 4.0L. I would think that if the whole engine is changed out that wouldn't cause a problem, as the secondary air system would be eliminated in its entirety. Same cats on either engine, (as near as I can find) so that shouldn't be a problem.

'99 Disco II
'95 R.R.C. Lwb (Gone...)
'76 Series III Hybrid 109
'70 Rover 3500S