stetsonaw, I'm not sure if this will work because you already removed Swype from /system/app, but to remove all remnants of Swype when it's still in system, you would go into Terminal and type:
su
sysrw
busybox rm system/app/swype.apk[or whatever the name there is]
cd system/bin
sh pm uninstall com.swype.android.inputmethod
cd..
cd..
sysro
sync
So I'm thinking that maybe you can still do these commands:
su
sysrw
cd system/bin
sh pm uninstall com.swype.android.inputmethod
cd..
cd..
sysro
sync
(the sysrw and sysro assume you have a ROM with those scripts built in -- if not, use whatever scripts/commands you need to in order to make system read-write, then read only again.
I hope this works, but I don't know for sure if it will!