88 Ranger 2WD 2.9 to 4.0 tranny question

[Diggerauditor]

My son blew the engine in my 88 Ranger, 2.9 186,000 miles, and I'm tired of this engine and lack of power so I'm thinking of doing the 4.0 swap. Found all the info except the tranny. I have a Mit 5-spd and most of the articles were for BII 4x4 with auto. I know the 4.0 will bolt up but my question is, does the donor eng need to be Manual trans or does it matter. Will my trans work or was there diff input shaft lengths that I need to worry about. If I get a auto trans motor, will my flywheel work or does that need to change also and will a std 4.0 clutch system slide in my bellhousing or will that have to change also. Most of the 4.0's here are auto trans so I kinda need to know before I go beating the bushes. Should I stay with a pre-93 motor or does it matter? Any help would be appreciated.

Sorry...M code trans, Mazda