Personally in your position with an empty engine bay I'd go for a modern engine. Of course it will take a lot of design work to get it all sorted out but you'll end up with more power and modern fuel injection, etc. (and that's from someone who has twinks in the Elan & Europa.....)
But I can see the originality idea, plus it will be a known path to follow so of course the twink does have a lot going for it. So, what to look for ?
Waterpumps - nothing like as bad as the internet myth. Ford internals, I've replaced both Elan & Europa pumps with no real hassle other than the fact you need to take off the head and sump to do the job properly. The fact that on most other cars the waterpump is an hour or less job is the main reason people mutter and grumble about them.
Heads - as you say they are all getting on a bit now. The manual gives head depth for normal & BV heads, something like 4.64" for normal, 4.6" for BV. The most you are supposed to take off is 0.010" from the BV head but of course you've got more to play with on the normal head. The Lotus manuals are usually pretty good on detail but the definitive resource is Miles Wilkins book on the TC engine, the main advantage being that it's written in light of the modern day parts situation. Apart from corrosion, replacing valve guides and seats are the big issues which would concern me, nothing difficult there but quite costly.
Plus of course the Twink in the Europa isn't the same as the Elan.
The front cover is different, the inlet cam longer to drive the alternator and the head/cam cover has machining to accomodate this novelty. That might make the search tougher as there were more Elan/Ford twinks than Europa ones kicking around. Is that Zetec looking better yet ?
If a twink is a serious possibility then I would suggest you look at either QED or Burton's website and look at component prices and do some sums. You'll then see why folks are asking £3/4k for rebuilt twinks and even more for modified race engines. If that doesn't put you off then buy Miles' book from Amazon, he's a real enthusiast and has great confidence in the engine which comes through in his writing.
Brian