Hi, getting a metal marker is pretty easy. any welding supply shop/fabrication supply shop (should) carry them. there are also yellow ink ones. ask for a marker that is especially made for marking steel/metal. I am not sure of where you live and how readily avalible you are to these type of places. here is a link to what I am talking about:
http://www.bakersgas.com/welding-markers.html
As for checking if the motor is good or not, you can do a out of truck engine compression test, this will require 2 ppl to make the process easier. check all 6 cylinders.
As for how long it takes to rip apart a motor: haste makes waste. you work at the speed you are comfortable with. also helps to take pictures for later references.
As for how far into ripping the motor apart depends fully on what you are going to be doing. I did a complete (no bolts left) rip down. However, I do/did have the lucky advantage of being able to pester 2 mechanics at work for guidance during my build. I did the build in the HD mechanics shop over a couple month period as time was alloted to me between working and spare time. (also what helped me out tons was that the shop already had all the specialty tools for the build... IE ring compressor, valve retention clamp, dial gauges... ) I suggest you find a truck work book for guiding you. (haynes, or... )
when I tore apart the 2.8 it took about 6 hours over 2 days, and that is completely dissasembled.
from what I can gather from you, you don't know how many miles are on the engine, and you aren't sure exactly what you are wanting to accomplish? Am I correct?
hope this stuff helps.
cheers