Congrats on your purchase, they are well built trucks.

About your questions

1. No it will not pass. Purchase a Mikuni at www.fcproducts.com
2. Yes ! http://www3.telus.net/public/dhuysman/vachose1.html
otherwise just find another running 2.6 and look under the hood. Sometimes that is the best way.
3. Depends on how you wheel, if your going rock crawling go strait to a ARB locker.
4. AC works great, bolt it back in, do a 134A conversion and your done !
5. Header may or may not be smog legal, There are two 2.6 performance gains worth doing. 1. TURBO 2. 5.29 Gears if you have 31 size tires or up.

Pictures of your truck ? We call 2 door trucks "SWB" for Short Wheel Base. The really have three doors <img src="/forums/images/graemlins/wink.gif" alt="" /> Any Montero with that is not SWB is called a "limo" <img src="/forums/images/graemlins/kewl.gif" alt="" />