Many Choices
Many people try and get an M30 engine with Motronic injection and 5-speed pair out of a late ('88 or '89) E24 or E28, as I believe this motor has 208 HP (the earlier mid-80s M30 has, I believe, 182 HP), and transplant the motor, 5-speed, Motrotrics (intake manifold, fuel rail and injectors, brain, and wiring harness) at the same time. I believe that the crankshaft position reference sensor is on the transmission bell housing, so the motor, the injection, and the transmission hang together as a set.
If you have a trani from an '85 5 Series, it may have the reference sensor already on the bell housing, or may have the the hole where it was removed.
Some folks don't like the look of the intake manifold that comes with the Motronics, and do the above but substitute the curved intake runners off an L-Jetronic motor from a pre-Motronic car like an E12 528i or an early 633CSi. I believe the fuel rail has to be modified to fit this manifold. I've never done it, but there are many posts on it. If I had money and needed to do another car from scratch, this is probably what I would do.
I have a mid year M30 (182 HP) engine with L-Jetronic injection from an E12 533i and a 5-speed from the same car. This is a simpler system than Motronics, but it has a conventional distributor requiring conventional setting of ignition timing. L-Jetronic doesn't use a crankshaft position reference sensor, instead getting position from the distributor. As such, it doesn't need a trani with the position sensor on the bell housing. As such, the injection system and trani hang together.
I could be wrong about any of the details in the above (except those pertaining to my own car).
There's nothing wrong with Webers if you like them and want to keep using them. Some folks feel that carburetors give better (more immediate) throttle response as compared with vintage fuel injection systems like L-Jetronic and early Motronic. It's hard to deny, though, that even vintage fuel injection is likely to give a better combination of easy starting, driveability, power, and fuel economy than carbs. I haven't touched my L-Jet installation in 15 years, and I can twist the key in the car for the first time in six months and it'll start right up, idle well, and pull away without stumbling.