All of the solder joints looked good except... you guessed it... U4. It had at least 3 shorts. I cleared those and tested. So far the power supplies all work and I can program the CPLD and the FTDI FT245R. I stopped when the on-board programmer failed to recognize the FPGA. I'm betting that is related to solder issues on U4. I'll try a bit longer to resolve U4's issues and if I fail I'll just bypass it and use an external programmer to check the FPGA.
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