Worked a little more on it. I feel I should clarify on a few things. The exhaust cam has been timed properly from the beginning, the issue only seems to be with the intake cam and I have a theory as to why that is. I have already removed the valve cover and the upper portion of the front timing cover to confirm my findings.
Here's the timing I started with before touching anything. 0 Compression for obvious reasons:
Here's what happened when I followed the FSM to the letter. This caused valve interference with the piston:
After trying to set the timing like a sane person, I went ahead and set the intake cam to the position where the cam lobes were lined up the way they are supposed to be. This threw out the window the idea of using any kind of timing mark on the intake cam sprocket. I turned the engine over by hand and there was no interference. I hooked up the battery and the compression gauge. Surprise surprise, I now have compression on all cylinders.
Here's my theory as to why this is. According to one post on Nico Club
(LINK HERE) regarding cams, apparently "the ?98 up intake cams had the dowel pin relocated to match the same 12 o?clock position as the exhaust cam has" so if the cams that I got were specifically designed for a 91-97 engine, then only the intake cam timing would be affected. Since this is a 2004 production engine, this kind of makes sense. Unfortunately I can't find anything on the Brian Crower website that would corroborate this so I may call them on Monday.
Has anyone else encountered anything like this? My plan is to just leave the cam where it is now and see what happens. Either way, I've spent the last 6 weeks trying to get this thing running and this is the only thing that seems logical.