Sounds like a short if its causing the clock to go out when connected.
Kenwoods (at least the two I have installed) have two power wires. The red one is the switched input and the yellow one is the continuous power. I think the power for the internal amplifier is actually drawn from the continuous power supply, not just used for retaining memory settings. I ran it straight to the battery (through a fuse of course) instead of on the standard radio circuit. I don't know how the harnesses are wired, I've never used one. I just get out the trusty wire cutter, soldering iron, and wiring diagram.
And, you definitely need to connect the ground line. Antenna is grounded too, but connect the wire.
Here's what i would do to troubleshoot:
Without the harness, you can try to connect just the 2 power wires and the ground and see if it turns on when you flip the ignition switch.
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