Auto to Manual transmission?

I want to start off by saying, If this has been covered before then someone please point me in that direction.
Now, with that being said, I'll explain the situation and go from there. I have a 2006 prerunner and I've recently decided that I want 4x4 and there isn't a huge market for high mileage pre-runners (180k) plus I already have a good bit of money in modifications that I won't get back if I sell it. Engine runs like it's brand new, so I've been looking into swapping it. I've priced out the parts, and will be doing the work myself with help of a buddy. But I've always loved driving a manual over an automatic and was wondering if anyone had done this before in a tacoma? I've seen and even helped out with a 240sx auto to manual, so it isn't a whole new concept to me. I figure if I have the truck in shambles, might as well do this. Will the trans from a 2.7l line up with my 4.0l? Sorry for it being so long, but I figured this would be the easiest way for me to get answers.

 

I appreciate, I figured it would be a whole 'nother animal than a 240. I'll probably just stick to an auto then since 4wd is my main concern. Trying to get a manual in there was just going to be an added bonus. Thanks for the input!