It takes considerable adaptation (including ECU and wiring) to convert a 2001 - 2004 Double Cab to a manual transmission. Yes, it has been done.

An alternative approach - which is arguably 'easier' - is to transplant a Double Cab cab and bed onto a manual XtraCab chassis. I know of 3 examples of this approach (2 4X4's and my Double Cab S-Runner).

Both approaches require substantial investment and effort. Unless you absolutely need the smaller pre-2005 Tacoma and the inevitable hassles of a highly-customized vehicle, IMHO you're probably better off getting a 2005+ manual Double Cab.