Hi,
[quote user="Nicholas Confer"]However, if i try to use either an external xds100v2 or the one on the docking board, I get the error and failed connection test.[/quote]
This is because the F28M35 controlCARD does not have the JTAG signals routed to the device - this requires adding jumpers from R40 through R46 (R46 is off picture).
(yeah, it is a horrid solder job - I did this ages ago, late in the evening and used a cheap soldering iron)
[quote user="Nicholas Confer"]If i power the external emulator and not the control card, instead of this error, I get an error telling me that the processor isn't powered, so it seems to me that this has to be something different from not powering the boards correctly.[/quote]
That is expected. If the device is not powered the external emulator can still sense that. The embedded emulator in the controlCARD, however, is galvanically isolated and therefore cannot sense power on the device, thus reporting a different error (unresponsive JTAG lines, as described by the OP).
Regards,
Rafael