Yeah, the ignition sounds like the anti-theft device was activated...
From what I recall, you have to leave the battery unhooked for around an hour, and it will reset the computer system.
(Wait, when you say the ignition wire, do you mean the radio wasn't turning on at the same time as the car, or the car wasn't able to start? I was under the impression that the ignition itself was not working).)
For the remote, you need to hook it back up through the Blue/White wire on the back of the HU, and then run a test light on the amplifier side of it. You need to know if the Head unit is properly supplying the power through the wire.
As an alternative (Not recommended, but it works), you can wire the remote wire through a full-time primary wire that is routed through a switch. It would allow you turn the amp off at any time you want by just flipping the switch. But, if you do this, you need to run a 5 AMP inline fuse in order to make sure that your car doesn't acccidently burst to much power through that wire.