I have a rusty 87 240 wagon that has a sound engine. It's quiet, doesn't leak, and has good compression. However, as I mentioned, the body is rusty. It also has a fuel injection problem that has cost me too much already. This car has a 5 speed transmission.
I also have a rust free 89 sedan. It has an engine that runs reliably but leaks everything, burns oil, and knocks. This car has an automatic transmission.
In the shop, I have a M46 overdrive transmission from an 84 240 turbo wagon.
This spring I am planning to put the engine from the 87 wagon into the 89 sedan along with a manual transmission. I have been searching the board to find answers to all of my questions, but haven't found them all yet.

1) I would prefer to install the M46 because I enjoy the overdrive and understand it is a better transmission. Would this be significantly more/less difficult than using the M47? What would I need to consider?

2) Because the 87 has LH 2.2, I understand the flywheel is different for the fuel injection on the 89. Do all 5 speed 240's from 89 and on have the same flywheel? Any tips on where to find one?

3) If I do use the M46, which clutch kit should I order? Also, could I just cut a hole in the bell housing to accomodate the flywheel sensor?

I'd greatly appreciate any help or ideas regarding this project. I'm trying to get the work on the 240's done early so that I can commit most of the summer to painting and reassembling my 69 144S. As a result, I'm trying to make sure I have everything I need at hand so I won't have a half done project squatting in my shop bay! Thanks!