This is a recent thread on just that.

Manual Transmission Swap

We are finally ready to do our manual trans swap into our coupe. I have successfully cured the Limpy-5th gear. Clutch assembly came from salvage yard. Throw-out bearing appears to be excellent. Bearing is tight and rotates silently. I see a little nick in the rubber there. Is there any reason I...

www.e46fanatics.com

That thread is well over 100 posts, mainly because of a lack of planning and research.

 

No offense but that is really confusing to follow and it doesn't really highlight the differences or lack there of between the E36 and E46 transmissions. I'm curious about the wiring and plugs on the tranny itself and getting it to work with the MS43

 

Yeah, you are right. Sorry, I think I just needed to vent my frustration after following that meandering thread. I kept mouthing: “WTF?”

So, regarding your question, @Effduration’s commemts in post #4 above hits it on the head (as usual).
Follow his advice.

 

You need to spend time on REALOEM.com and look at both E36 325i and E46 330i. Focus on differences in transmission models, trans mounts, driveshafts, guibo and differentials. The connections between driveshaft and transmission and driveshaft and differential are likely to be a challenge.

sourcing all the manual swap parts from an E36 for an E46

it will Likely work, but is likely NOT plug and play..

 

The transmissions for the two cars are the exact same. The trans mounts and driveshaft can be pulled from another E46 along with the differential. I couldn't find much information on the guibo or whether or not they were different. If I'm not mistaken the differentials in the E46's are all interchangeable correct? I thought you were able to use the rear half of any driveshaft because they are all identical.

 

Your E36 325i driveshaft's rear diff flange will have 4 bolts whereas your E46 330ci's rear diff needs a driveshaft with a 6-bolt CV joint.

Pictures below from FCP Euro (check the fitment notes)

E36 - Lower left corner is the diff flange - 4 bolts:

E46 - Lower right corner is the diff flange (that's in your current E46) - 6 bolts through a CV joint:

Hope that helps.

OURMANDAN was having a lot of trouble at the start of that linked thread because he sourced a pedal bracket and pedals from an E36 and there are subtle differences.

So my advice is to try and source a pedal assembly (and really, as much as you possibly can) from an E46 around the MY of the car you're swapping into, to make sure everything stays happy.

 

Yes I just finished ours yesterday ... we used an E36 transmission and also pedals .. well that's a story,
Its been on stands since just after Christmas .. but this morining we finally fired it up and tested the gears & Clutch!!
Tomorrow its off the stand!
There are several things you must take into account, but at the end of the day the BMW 5 speed fits almost exactly with one drivetrain issue that you'll need to deal with. I will be your resource on that because I just deal with it and need to pass on the great assistance others have provided. I see several of those folks already responded to you.

Be sure to read my EWS post ... especially if you are watching the 50s kid videos. I can save you 2-3 days of pain.