Timing off 180 degrees?

Trying to start my kz1100 after top end rebuild. I'm getting a lot of backfiring. I'm thinking it may be out of time. I went through all the required positioning of my valve train and timing chain. Number 4 lobes facing one another, Exhaust arrows pointing forward, Intake to the rear, 44 pins end to end as well as the notches on the right side of the cam in position. With the positioning that is done can the timing be 180 degrees off?

If you had the 1-4 "T" mark lined up, then no. But you could have the wiring off. The coil wiring could be swapped around. So then 1-4 is firing when 2-3 should be. Not to hard to see, just swap the primary wires to the other coil.

What do you mean the primary wires? Are we talking about the small wires that plug into the coils or the plug wires?

Small wires. Plug wires are probably set closer to length, so they won't swap out to easy.
have you checked compression? You can turn the motor by hand and see when #1 has compression. Then rotate to the 1-4 "T" mark it shouldn't be far away.

There is no way to know if we are at #1 compression or at exhaust w/o taking off the cam cover to see valve location is there? I mean I will if I need to but don't want to if I don't have to.

Sure its easy. Take off your Ignition cover, use the 17mm head nut to turn the motor in direction of normal rotation. With the #1 plug out, you will hear the air pressure escaping. You could hold a finger over the plug hole and feel the pressure building. Unless you are off on cam timing or valve adjustment, you should have compression here. Line up the 1-4 "T" mark when you feel the compression on the #1 plug hole. That will be #1 TDC.
When you get it lined up, look at your Ignition, the Rotor lines up with the Pick-up coil. Should line up with the rear one, towards the back of the bike, or left side as you look at it.

Thank you my friend. So if my timing is good, switch the wires on the coils? Do the wires have +/- polarity? Been worrying about this all day. Now I can worry about other stuff.

No the coils don't have a polarity. Although some are marked + and -, many are not.
Did you look to see where you ignition rotor was pointing when on #1 TDC?
On your Ignition coils, the Red and the Black wires should be on the coil you have the 1&4 plug leads on. Green and Red are for the 2&3 coil. Look at you Ignition Rotor, it should be facing back towards the rear which is the 1-4 pic up coil.
The service manual link in my signature has all of this info and lots more.

No I gotta turn in I'll check after work tomorrow. Thanks

Couldn't sleep ........ much. Woke up at 5:00, checked my timing which was good, switched the coil leads and VROOOM.

Sweet. Hopefully you can go ride now.

It won't affect the way it runs, but you may want to confirm everything is set up like it was from the factory for easier troubleshooting later.

For the large inline 4 motors:
Ignition rotor points backward (towards the pickup with black and blue wires) when 1&4 are at TDC.
The left coil is for spark plugs 1&4, and gets the black wire.
The right coil is for spark plugs 2&3 and gets the green wire.