The 5.3L & 4L65E going in my Wagon project cost me $2700 delivered. I've another couple hundred in flashing the PCM to remove the nanny and body functions, but that includes the guy tuning it once running so that the shift points are correct, etc. I'll have some more money in getting the trans configured with a 4WD output, but that's on me as I could have gotten a 4WD version for my source had I not switched what the combo is going in. Origianlly it was going in my '73 SBSS Chevy C10, but the TBI 350 in the Wagon runs so good that I'm going to move it to the '73 instead.
Nothing wrong with the stock engine management on an LS engine IF you're not going to lean on it hard. For a stock or nearly stock engine I highly doubt that anything aftermarket will be as good. I'll guess that GM put 1000's of man-hours into testing and tuning that system. That is not something easily duplicated at home with an aftermarket ECM/PCM.
If you're going to boost it, NOx it, or seriously modify it's internals, then I doubt that the OEM PCM is the ideal tool.