I'm wanting to do a high flow cat to replace an oem 99-00 EX/Si cat.

The oem location of the secondary 02 sensor is right in the middle of the cat.
Can I put an 02 bung AFTER the cat instead, will the secondary 02 sensor still read what it's supposed to?

I also have found a Magnaflow universal cat that has an 02 sensor on one end of the catalyst area but right on the corner, not sure if that'd go in the front or rear when installed.

 

Put the secondary 02 sensor after the cat.

 

^ Agreed. The secondary o2 sensor should be placed after the cat so that way it reads if the cat is working properly or not. If it is placed before the cat then its function is the same as the first o2 sensor.