Wow, well it seems like you covered most of your bases. I doubt very much that compression is your issue if the car runs normally most of the time. How many miles are on the car at it's current level of tune, would there be any reason to even suspect a blown motor?
Fueling definitely sounds like it could be an issue, since a slight hesitation could be indicative of either a dying fuel pump or a clogged injector, but if the car runs normally most of the time and starts on a cold motor I would doubt very much that your pump is kaput.
Since you're doing the compression test, check the coil packs (swap them around cylinder to cylinder see if anything changes), then maybe check to make sure everything is installed/clipped/torqued properly. It's weird that you're getting what sounds like a characteristic misfire but not throwing a code. Any chance it's the open loop/closed loop transition of a UTEC that is perhaps causing some hesitation? It can seem intermittent since you're rarely at the same load site every single time you accelerate through an RPM based on where your foot is on the pedal.
Sorry I can't be more helpful, but this is really an oddball problem. If you can't find any good answers, try PM'ing the description of your problem to either RiftsWRX or AZscoobie on Nasioc, they might throw you a bone and have something helpful to try to diagnose the problem.