"I feel your pain ..." the Martin kit offers us all a chance to practice our coping skills.
First, I believe you looked at the wrong page on KitGuitarBuilder.com -- the dovetail joint is covered in the Martin Kit Instructions, since my Stewmac dread was a bolt on. Here is the page with the dovetail fitting explained.
I've re-ordered your questions as I understand them to put them in the order they should be addressed:
4. Right now when I insert the truss rod into body, it hits the very top (or bottom as it may be) of the top plate. The threaded part goes barely into the top bar. Do I need to chisel a bit of the top plate away to fit the rod farther so that the threaded part goes all the way through the top bar?
>>Until you get the dovetail joint fitted correctly, you should not do anything at all with the truss rod or its fit into the body/top. Eventually you will want to open up a slot for the truss rod to clear (see below).
2. When I adjust the dovetail to fit correctly to the body, I canâ€™t see a way to insert the truss rod into the body and put the neck into the dovetail at the same time. Is the plan to install the dovetail fit and then slide in the truss rod and glue it and then glue on the fingerboard? What is the best glue for the truss rod? Epoxy or Titebond?
>>If I understand your question, your joint is fitted at this point. You will want to create the neck/fretboard/truss rod assembly as a complete unit before installing (gluing) the neck joint. On the Martin Jumbo kit body, it was necessary to cut a slot (5/16 inch wide, length as necessary) into the top to allow the neck assembly with truss rod installed to mount to the body. It was also necessary to remove the truss rod bolt and put it back on through the soundhole. It worked. The neck with fretboard attached slides into place by a hair; it has to be done delicately. (GLUE: I've used epoxy on all of mine.)
1. The dovetail joint is very delicate and precise. Once you get a dry fit that seems perfect, wonâ€™t the addition of glue on that joint ruin the fit and make it sit too high? What is the best way to glue it and in what order?
>>at this point, you will have the joint fitted perfectly, the neck assembly completed, the slot cut, etc. The glue, if you do it right, will only add about a micron of thickness to the joint, if that much. It isn't something to worry about if properly glued.
3. When I look at the diagram in the Martin documentation, the rod is glued into the routed channel in the neck and then it goes through the neck block. At the end of the rod is a washer but this washer seems to be free floating and not connected to any part of the body. If this is the case, how does the truss rod work if it doesnâ€™t pull against anything?
>>You're correct in part, but the system works. The washer is pushed against the end of the truss rod by the bolt when you need to remove relief from the neck. The truss rod is firmly glued in the channel, and the neck provides what the washer pushes against, causing the rod to hump toward the surface of the fretboard, bending the neck "backwards." When you are adjusting the neck in the other direction, the washer is a "stop," and merely holds the neck in a certain relieved position.
1) Fit the neck joint.
2) Fit the truss rod to the body
3) Clamp or rubber band the fretboard to the neck, with truss rod installed, to be sure the assembly can be mounted to the body.
4) glue the truss rod
5) complete the fretboard and glue it to the neck.
... eventually, glue the neck joint when that step is reached.
Hope this helps some.