Checked the Paula analog bias voltages as requested... they are +2.31V and +2.34V respectively.
I'm going to remove the RTC and U177 as suggested, and also some of the SIMM sockets for the fast ram (two for sure, maybe three), since there is some corrosion under there. Once I do that, I think I'm going to go back to basics and check the typical stuff.. power supplies good, resets, clocks, and also check the serial data from the io shift registers to see if they are any good.
I may also check that the keyboard data makes any sense too, just to see if the aftermarket keyboard is sending Amiga scancodes.