OK - I just saw this one...
First off, you are letting yourself in for a fair bit of work. If you have your heart set on the deep first gear, I'd probably think NV4500 - MistWolf can help you with what you need to install it.
For a swap from an auto (I don't understand why, but I don't know what you've done to your engine yet, either!) you will need flywheel, clutch assembly, clutch master & slave cylinders, donor pedal and linkage, transmission, correct transfer case (probably easier to use an Atlas than a D300 if you have the option,) and expect to have new driveshafts made as mentioned above. Now would be a good time to do those yoke upgrades you were thinking about as well, and toss in the SYE kit since you ahve everything torn to bits already!
Mountings for the clutch setup should not be a problem (the firewalls for autos have plugs put in the holes not used) but you will find some of the spots you try to work in fairly tight - especially under the brake master cylinder when installing the clutch master. Expect also to have trouble with the transfer case shift linkage - which is why you are in luck thinking about the twin stick version of four-wheel drive. I'd also expect some crossmember fab or mod to take place as well.
This is all edjamacated guesswork (similar to a SWAG) since I've not done the conversion myself yet (and before you ask, I plan it as part of a restomod job anyhow, so I'll have room to work!) If and when you do the job, would you please document? I'd be interested in hearing how it went for you!
5-90