The 87-91 YJ's came with an ECM. Its mounted on the back side of the driver's inner fender, down below the coolant tank.
If you switch to this drivetrain, you can do a nutter bypass, but you need the PCM from the donor vehicle. The one from yours isn't compatible. And as you thought, you will lose the use of your gauges.
Seems to me like a lot of work to go back in technology. Fuel injection is much better than a carburetor any day of the week, and although the older YJ has a 4.2L motor, it doesn't compare with the horsepower and torque of the newer smaller 4.0L.