That's basically it. And that 350 psi is what they call margin pressure.
So I took the machine out yesterday with a fresh mind and a better understanding of the how an axial pump like this works. hooked gauges into the load sense port and the pump discharge port. Fired up the machine and saw that the pump discharge was around 750psi and the load sense was 0psi. Ran the machine around for a bit, worked all controls had had the bogging event regularly. The entire time the machine was operating and not bogging i saw ~750psi of margin pressure. I was able to confirm that at the bogging event the machine would surge the discharge pressure to ~4200psi and when I let go of the controls the load sense would drop to 0psi but the discharge pressure would stay hung up at 4200psi. If i bumped the controls a bit i was able to "knock it loose" and it would go back to normal. I decided to address the margin pressure first as that was adjustable and would start to eliminate causes.
This is where it got interesting.
I found the margin adjustment on the load sensing valve and went to loosen the set screw, it felt like it was hand tight at best, loosened it about 2 turns and adjusted the valve about 1-1/2 turns(247 psi per turn). which would give me the 350psi margin pressure. I went to tighten the set screw and it took nearly 4 full rotations to tighten it back down. Very odd. I did also notice at this time that the entire pump was painted OEM back, but this load sense valve was rusted like it had been replaced at some point.
Hoped in the machine and fired it up. Pump discharge ~350psi, load sense 0psi. Perfect. Ran the machine around and did some digging. Did not bog one time, pressures never got hung up like before. No matter how hard i pushed the machine or tired to get the bogging event to happen it could not do it. The machine ran like a top.
I am going to run the machine some more before I call it fixed. But I think that has resolved this issue that i was having. I can only imagine that at some point that load sense valve was replaced or adjusted, and that set screw was not tightened back down correctly. Over time it worked itself higher and higher. This would not really be noticed as it would not slow down the movement or lack power. It kept creeping until the point that the limits of the pump were reached and something was hanging up. My thought currently is that the swash plate was "hyper extended" and the angle created between the swashplate and actuating rod could not be overcome as easily. This would explain the random occurrence and the slow period over which the issue arised.
Again I am 98% sure that this issue is fixed but I am 100% sure this troubleshooting would have been much more difficult without your help. Thank you for your quick responses and extremely helpful graphics, procedures, and descriptions. I feel that i have not only fixed my machine but have learned much about the hydraulic system that will be of benefit in the future. Thank you again!