I've added my comments below. I have done the reverse of this job, so be aware it is a major undertaking.

M46 trans: Consider an M47, that way you won't have to worry about the OD (true 5 speed)

m46 bellhousing: Comes with the transmission.

new clutch pack: Yes

clutch pack bolts: Yes

m46 flywheel: Yes, and spacer plate

flywheel bolts: Yes

new pilot bearing: Actually, a pilot bushing

new throw out bearing: Yes

Cluthc lever.: Even if the trans you get has one, consider a new one as they have been known to crack/fail.

clutch cable: Yes, factory only for reliability.

manual pedal box(Is sheet the metal pedal box welded in or is it bolted in??)
manual car brake and clutch pedal: Replace the entire pedal assembly. Also consider replacing the firewall plate as well, that way all the holes will be there.

ecu?? ( Is there such a thing as a manual or auto ECU ???): No, your LH2.4 ECU will work fine.
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2. What do I need to change in the driveshaft area ??: The driveshaft.

3. Which cross member do I use and are the trans mounts compatible??: The cross member is compatible, it just uses a different set of bolt holes in the floor.

4. how do I adapt the auto trans reverse back up light switch to the manual ?: You may find the wires are already there, you also need to take care of the neutral switch.

5. Will I run into any problems with rear end ratio? ( I have 3.75 rear gears):Unless you want to run some high RPMS.

6. Since this is a 92 I have the electric mag speedo pickup, what do I use to plug up the speedo gear port on the new m46 trans..: Get a rear axle from a 91, 92, or 93 manual car with ABS, that will take care of your sensor. Use an M47 instead of an M46 and there is no speedo hole issue.

Looks like you are in VA, I'm in Western NC. As I mentioned, I converted our M47 92 to an AW70, except for one part and that is the rear end. In short, I'm running with low torque and low RPMs as a result. If you are interested in swapping rear axles let me know, I think I still have an M47 driveshaft as well.
Let me know and I'll do an "inventory on my "leftovers" from the conversion.

jorrell
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92 245 245K miles, IPD'd to the hilt, 06 XC70, 00 Eclipse custom Turbo setup...currently taking names and kicking reputations!