Congrats on the upgrade to Extra Class.
It sounds like you didn't wire the switch contacts in series with your +12V power, but instead you have the +12V power and ground going directly to P1 on the board. If you want the on/off switch to turn the radio on and off then you'll need to run the +12V leads from the rear panel power jack to one side of the pot-mounted switch and then another wire back from the other side of the switch to the +12V connections on P1. The connection diagram shows a switch in series with the power lead - that switch is the one that is part of the volume control.
As far as not being able to tune when the mic is plugged in, it definitely sounds like the radio is going into transmit mode when you plug in the mic. You can't change frequency while the rig is in TX mode. Remove the mic and check between the ground of the mic plug and the ring connector. I'm betting your ohmmeter will show a short there.
As far as initial setup - I had to do the BFO frequency adjustment on my radio when I built it. This involves putting the radio into setup mode and then selecting BFO adjustment from the menu. Then you turn the VFO knob until the audio passband is in the right place - basically until a sideband signal "sounds" right. If it's too far in one direction the audio will sound very tinny with no low frequency response. If it's too far in the other direction it'll sound muffled. When you're happy with the setting you press the PTT button once to save it. So you're gonna have to fix that mic short before you do this part since you need a working PTT button.