I made real progress today!
I disabled the aftermarket alarm first by removing the control module, and cutting all wires that were attached to the ignition. This had no affect on my starting problem, but it did clear up my electrical short. Next just for kicks, I swapped out my starter relay, and ruled that out as well. So, I leaned on trusty old Supramania for advice. A quick search suggested if I hear the relay click, that is is either starter or starter wire. So, I then ran my positive battery directly to the starter, and found it to be a bad starter. Now my hopes are that once I replace the starter, this thing will spring to life. Last I looked around here for a starter, I couldn't find one. But, I feel like I do have one somewhere. If not, I will be getting a new one soon. With my EGR removed, I'm not so scared of a starter swap. So, as soon as I get time, maybe I'll have good news.
Oh yeah, I almost forgot to mention fluids. I also got 5 quarts of Royal Purple into it today. And, I topped off my tranny with a quart of gear oil. Still gotta put the shifter back in though.