"before the ignition swap"
What are you doing, i.e. what's the "ignition swap" about? Your problem is likely associated with the 100 ohm resistor in the ignition switch. You're probably getting a C42 FI error.
Yes and I don't know how to connect the ignition wires. I wrecked my bike bout 2 months ago and rebuilt it n the old ignition was broke in the wreck so I was just turning the tumbler with a paint can opener and I got the ignition I ordered off eBay but it's got an extra wire and the plug was wrong so I took the plug off the old one and was going to put it on the new ignition but my fuel pump doesn't come on when I turn the key on and the kill switch on and it worked just fine before
The ebay switches come from China and don't include the resistor. Without it, the ECM thinks you're a crook and won't activate the fuel system. The O/Y lead needs the resistor but I have no idea what the leads are on the ebay switch. You would have been better off buying a used Suzuki switch.
Here's a genuine Suzuki switch that ought to work. It doesn't have a key so you'll have to get a locksmith involved. Tools like the Accureader make that a easy task. However you'll end up with one key for the ignition and another for the gas cap and rear compartment. I think it's possible to change the tumblers so you're back to one key but no guarantees. A good locksmith ought to know. It's being sold by someone in my town but I don't know who it is.
I hesitate to get you further involved with Chinese locks but there are things like this and this on ebay that look attractive but I don't know for sure. They're coming from US sellers so returning them won't be a huge deal. You can also ask the seller if the lock has a 100 ohm antitheft resistor on the O/Y lead. It could be added if it's missing. The first link says that it has five pins. The Suzuki switch has seven so they either are in error or it's less secure. The second link includes the gas cap and rear compartment locks. That's nice as it avoids the two key issue. But at that price, I wonder what you're getting. Note that both have the correct wire colors and connector.