I believe I have a wealth of information on this topic and have been wanting to share it for years (and record it in one place for myself), but I could never get myself organized enough to do it. So I am finally getting the ball rolling, better late than never, and will slowly fill everything in. Please be patient.
The Mazda M5OD-R1 (a.k.a. M5R1), and it's upgrade, the M5OD-R1HD, are the manual transmissions that will bolt up to both the Ford 160hp 4.0L OHV and the 210hp 4.0L SOHC V6 engines.
The Borg Warner 1354 Manual is the manual 4x4 transfer case that will bolt up to the Ford 4.0L V6 manual or automatic transmissions.
I am a "manual" connoisseur. When car shopping in 1999, my two criteria were truck and manual transmission. This brought me to the Wrangler and the Explorer. A test drive sealed the deal. When signing the paperwork, the dealer broke the bad news that the manual, at the time, was only available in the fully stripped down version with the weaker OHV engine. I settled.
With the help of this forum, I converted my SOHC engine to a manual transmission and it was the greatest thing I have ever done in my life. I am now in the process of converting my BW 4405 electric automatic transfer case to the manual.