As you said, that ECU is for a 1G DSM Turbo AWD (D27A), model year 3/89-6/90 - MD145903
And yeah, it should explain a lot of issues. I'm surprised your car runs at all with this ECU. I'm actually running a 90 ECU in my GVR4. All you need to do is swap ECU pins 14 and 6. The easiest way to do this is cut both wires, and put crimp connectors on all 4 wire ends. Then, just plug pin 14 into pin 6, and vice versa. Normally, I always solder my connections, but if you want to be able to swap back quickly for troubleshooting or whatever, the crimp connectors work best.
As far as ECMlink goes, your ECU is not an EPROM, so you'll need to have ECMtuning convert the ECU to take a chip if you want to use that ECU. They offer this service alone for $135. However, if you purchase ECMlink tuning software, they will give you the same service for only $95. Sometimes, this is the better route since EPROM ECUs are either hard to find, or overpriced.
It really just comes down to what ECUs are available, and their price. If you can pick up a non-EPROM ECU for around $100 bucks, you could then buy ECMlink tuning software and also have ECMlink convert and socket your non-EPROM ECU. In that scenario, you would basically get an EPROM ECU for $195 bucks out the door. It's not often you find a used ECU that has been socketed for that price.
Most of the time, you will find guys selling ECMlink V3 with an already socketed ECU all together. Packages like that usually go for around $550. Honestly, that's the way I'd go. Keep the ECU you have for a spare, or sell it to recoup some of your money. Keep and eye on the classifieds here, and on DSMtuners.com and wait for someone selling their whole ECMtuning package used. Try to find a price between $500-$575.
Here's ECMtuning's page with the pricing I was referring to:
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