Since you're considering an engine swap along with some other mods, you should know that the resale value of your car will be less than a similarly prepared original car.
Having said that, I think the Zetec is the best engine swap because as Andy says, there are fewer modifications required and the engine is readily available. In fact I think Ford sells crate Zetecs. I believe there are several different flavors of Zetec DOHC motors but I'm not competent to advise you on which one. One thing you will have to decide is if you're going to use injection or carbs. As Andy says, the Zetec will require the TC bell housing.
I would advise getting an NG3 transaxle. It will bolt directly to the the TC bell housing but there will be some modifications required on the rear hoop for mounting it there as well as new shift linkage. Parts are more available and it should be strong enough for any normally aspirated Zetec you'd drive on the street. They are sometimes available at salvage yards (check out
http://car-part.com and
https://www.carmonkeys.com. They came from the later model Renault Turbo Fuego). There are also modifications required to the tranny that are explained here:
http://www.greytower.com/jon/lotus/europa/gearbox/gearbox.html. Banks (
http://www.banks-europa.co.uk/index.php) sells them ready to go (with shift linkage kit and rear mounts)
There are several different rear disk conversions described here:
http://lotus-europa.com/manuals/ (as well as a lot of other good information including the parts and workshop manuals). Banks also sells a vented front disk kit and rear disk kit.
There are some rear suspension mods that people do. Banks sells a twin link kit and Richard Mann developed his own twin link suspension but it may take a bit to find the particulars on it. Banks, r.d. enterprises (rdent.com), and Spyder (
http://www.spydercars.co.uk/category/spyder-products/spyder-lotus-europa-products/) sell tubular front A-arm pieces. Dave Bean probably sells tubular A-arm pieces, too (
http://davebean.com).
Spyder, Banks, SJ Sportscars (
https://www.sjsportscars.com/home.htm) and probably Dave Bean all sell frames. The Spyder frames are space frame design and support their own rear A-arm suspension. I think they can be had to directly support the NG3. Banks makes their own frames. I suspect everybody else sells Lotus frames.
As for which Europa to use as a platform, I'm not sure it matters much beyond Andy's warning that a Zetec will require some modifications to an S2 frame. The TC should give much better rear 3/4 vision but some don't like the chopped rear wings (I don't have that problem).
My advise is to look over the documentation page I mentioned earlier (
http://lotus-europa.com/manuals/), the Banks, r.d., and Spyder sites to see what they have for you and ask a lot of questions. Since I have a TC, I can't give you a lot of information specific to them but there are people here who can. I didn't mention an S1 as I think that is a lot more complicated a restoration since its frame is glassed into the body. There are certainly some sources I didn't mention but that is because the ones I did mention are more familiar to me. I don't mean to be exclusionary.
This is a great Europa forum. I think joining the Yahoo lotuseuropa list is valuable, too. One other site that you might find interesting is Dave Anderson's site about his Europa (
https://www.prevanders.net/europa/index.html). He extensively documents the things that he did to his car and he did a lot. One thing to note about his car is that it recently sold on Bringatrailer.com and in spite of the interesting and apparently well executed mods, it only sold for $15,000. So I stress, do your mods with your driving enjoyment in mind and forget about any increase in value.
