Update: Problem Solved
It was in fact a bad ECU. I put a new one in and it cranked up without any hesitation.
I learned a couple of useful things from the experience. First, apparently anytime you take a Caterpillar engine to an authorized service center they read the computer and make a record of all the settings. This worked in my favor because after getting a Cat Remaned ECU they needed to "flash" it, or program the computer with parameters for my particular engine setup. Sometimes they can download a file with all of the factory parameters, in my case they were not able to locate that file.
Because I had it serviced in Phoenix over the summer, although I was in St. Louis they were able to download all of the parameters that they read from the ECU when it was serviced in Phoenix and program those into the new ECU. This saved me from having to have a tech come to my rig and assess the engine configuration and guess as to all of the parameters.
The second thing I learned is that I've been seriously abusing my house batteries by discharging them too much while boondocking. My generator is not currently working so I've been recharging using the main engine. This has put too much strain on the alternator which is what caused the voltage regulator to fail, resulting in voltage surging too high and frying the ECU. This makes the list of "Things I Wish I Knew".
