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Some type of closed loop injection might work, wouldn't it? If you install O2 sensors, then the injection system should be able to adapt. Would VE still affect this? I don't know a whole lot about FI, so I'm mostly talking out of my ass.
Nope. Any of the OEM EFI systems will rely on a narrowband O2 sensor, so the loop can only be closed at a mixture of 14.5-14.7:1, which is fine for idling and low loads on a water-cooled engine, but is completely inadequate for good power or an air-cooled engine. Nearly all EFI systems go "open loop" past 1/2 to 3/4 throttle, as well, since you have to run richer than 14.7:1 with nearly any engine to get good power.
All of the OEM EFI systems I know of that use a wideband O2 sensor use the sensor to run substantially leaner than 14.7:1 during cruise, and the engine is adapted to run this lean safely. Such lean-burn engines are one way a lot of automakers have acheived the low emissions levels seen in some current cars. Running a Type IV this way would kill it in short order.
If you're REALLY into DIY and really cheap, there are a number of people who fooled around with reprogramming a common GM ECU to remap it and tune for other engines. Indeed, Bruce Bowling and Al Grippo, who designed Megasquirt, were active members of this group. It's a hard slog, and MS is actually substantially easier to deal with, and really isn't all that much more expensive (considering the tools you need to reprogram a used ECU).
I'll generally agree with the position that you should try to just fix the D-Jet. Stock and properly functioning, it works well, and has no serious "deficiences". If you desire to do things to the engine that makes life difficult for D-Jet (like a wild cam or a big engine), then MS is a route that would be much easier than trying to adapt a junkyard system to the Type IV.
CIS is a nice option, and you can pick those systems up in a junkyard in operating condition (look in any 80s VW). Unlike EFI (CIS is mechanical), CIS really can adapt itself to another engine with the same number of cylinders, since it measures the airflow into the engine at all times. The curve of airflow to mixture is somewhat tunable (at least the "height" of the curve). The downside of CIS is that you can't run a cam any wilder than what D-Jet will accept, so you're really just swapping one relatively limited system for another.