All 1.8 16v engines were CIS-e and all 2.0 16v engines were CIS Motronic. Only the ABF sold in Europe had a multipoint EFI system. I think CIS-e is a decent system, but can get finicky. CIS-m is pure and utter shit. Both the 1.8 and 2.0 had forged internals with oil squirters. The 1.8 and 2.0 heads started out with the same casting. The differences are in the valve sizes with the 1.8 getting larger intake valves, but smaller exhaust valves. Only reason to put out the effort to get one is if you're going for NA only power. It doesn't matter much in boosted applications, unless you're just going for ubber horsepower freak status. To lower the compression on a 16v get some head studs and either double stack head gaskets or get a head spacer. There are plenty of cars out there in the 200-400hp range that do this, and plenty of name brand turbo kits for VW engines that use head spacers. Only time anyone ever has an issue is from their own stupidity with not being able to use a torque wrench. Anything above 350hp and I'd say replace the rods with some H-beams, and you may as well do pistons at the same time. You can cryo treat the crank if you want, but you'll probably snap the block at the intermediate shaft from high HP before the crank goes.
Doing Megasquirt on the old 16v engines is a bit more involved than just buying the $150 MS1 kit. You need to build a wiring harness and create from scratch a new fuel system for the car with custom components (only component you can reuse is the fuelpump. everything else including the where the injectors go into the manifold has to be replaced). 3/4s of the money I spent on the MS2 setup on my old 16v was on the fuel system. Trying to save a buck with ebay stuff will just send your car up in flames. If you're patient you can sometimes find some good parts off of the classifieds on Vortex that someone just wants to unload.
To run an 02a in a mk1 you either need to do what rotundapig did in his GTI and run the clutch mechanizim on the transmission from a eurovan (02a transmission that used a clutch cable) and a CRX clutch cable (eurovan one is too long and has the wrong end for the pedal. Oddly enough a honda one works), or get really good at metal fabrication. You'll need it because you'll have to build a hodgepodge system from both the B3 and A1 pedals and MC system along with hand built metal bracketry. You'll still need to buy custom mounts or fabricate new ones to mount the transmission.
