When I changed the DOHC engine in my 4be to a 2.9, I just sent DVLA a receipt from buying the engine. All they seem to be bothered about is that the new claimed engine size is legit and that the engine isn't stolen, not whether it's been fitted properly.

If you don't have a receipt, just write one out on paper, including the engine number, claiming you bought it off someone on ebay a few years ago.