I just did my winter hard top for the season, hooked up the plug for the rear heater and it works but it's cranking out cold air even when I am up to running temperature. Front heater is blowing lots of heat. Am I missing something? Is there something other than the plug I need to hook up?

What do you mean "hooked up the plug for the rear heater" ?

The console heater?
Why was it 'unhooked' ?
What year truck ?

89 4Runner, had the heater unplugged from the center console for the summer, along with the window switch, and the wiper as I had no hard top on for the summer. Getting my thermostat changed out tomorrow.

OK, I understand now. I take my hard shell off in the summer too, but I don't disconnect the console heater.
If you're getting normal heat up front, the t-stat is OK and you should be getting it in the rear. Are you getting coolant flow to the rear? Maybe there's an air pocket in the lines to the rear.

That's something I would not have thought of. Airlock to the back line.... I am draining out my coolant, replacing it and giving a good radiator flush. Should fix it. My mechanic seemed to think that my front heater was working normal, so I guess I'll soon find out.

Replaced the thermostat, found my rad cap was leaking. Replaced it, now it runs smooth, temperature is good driving around but once warm and sitting idling the temp goes up. Front heater is pounding hot air, rear heater is still totally cold. If I move the temp switch up or down it slightly changes for a second and goes back to cold.

I found a bit of coolant under the rad cap on the top of the rad after turning the rear heater on today. Otherwise the cap has been dry for days. Is this an airlock? Can I run the truck cap off until I get some heat? If it does not get hot what is the next step?

Appreciate any help
Thanks

What year? The heater systems alot of times need to be "burped". That is accomplished before pressure is built up the top heater core hose loosened enough to "burp" the air that is trapped in the high spot of the line.
Air locks air usually result in both heaters not working so you may still have a flow issue to the rear heater core.

What year?

He has a removeable top, therefore it's an 84-89.

Does coolant flow through the rear core all the time or does it have a flow control valve that is operated by the rear controls? I ask because my Camry adjusts the temperature this way and not by a bypass flap. If so, the valve could be stuck.

Does the coolant flow through a rear core? Is there a control valve in the rear? I don't know for sure. Only release screw I found was bottom front under the rad. I did find out today that it is my rad cap leaking again. I did just replace it, 13psi is right for the rad cap right? My overflow tube is quite long and in a big S. Could this be too long and have to push too much pressure for the cap to hold? Seems it comes out the cap and it's not getting to the overflow resivoir. Could this be right?

Can I "burp" the system by just leaving the cap off the rad and letting it come up to temperature or do I have to take the top hose off?