When I got the bike I had no key. So I bought the ignition tank lock combo that came with keys. The connector on the ignition is completley different from the old. So my question is, I have seen people saying just twist the 3 wires together and put on a switch. So does it matter which wires go where when splicing in the factory plug to the new ignition?

 

No, you should just twist all 3 wires together.
Your bike would always be on then.
Also twisting wires together is not a good way to do electrical.

Easiest thing to do would be swap the connector from the old ignition switch to the new switch, then just plug it in.
Or you could also wire in a waterproof toggle switch. This is what I did on my racebike.

Your 3 wires are:
Red - power come in from battery - always live.
This should be on 1 side of the switch.

Red/Black stripe - out of the switch to fusebox then to rest of bike.
Blue/Orange stripe - out of the switch to fusebox then to radiator fan.
These 2 wires can be wired together.
They both feed power to the bike once the ignition switch in turned on.
They should have no power when the switch is off.

 

Thanks man, got it figured out the door now. Basically turned out the door now exactly as you said