1997 Dodge Intrepid Warm car idles rough and smells of gas

This is an emission problem. You should get a code. if I am to guess, instead of your EGR, check your EVAP system: Purge solenoid valve and/or canister.

CEL is now on. Had it scanned today. Got P0302, P0306 codes now. Gas smell may be from flooding?
Going to change spark plug wires and plugs.

You should not have any fuel smell or "flooding". I would test for fuel pressure, after you replace the plugs.

Replaced the plugs, wires, coil. Ran great for two weeks!! This week started again. Runs fine cold. After warming up (about 3-4 miles) runs rough, idles rough, misfires throwing codes P0302, 304, 306. No gas smell, but do smell exhaust while sitting idle. Noticed some holes in catalytic converter. What's confusing us is the fact that the misfires are not consistent. Always misfires in the morning after warming up. But then runs great after sitting for an hour or so. Misfire driving home from work after sitting for several hours.

P0302, 304, and 306. Those are cylinders 2, 4, and 6. They are all on the same cylinder head. I suspect that you have low compression on that head. I would do a compression test and a leak down test on the cylinder head. Whatever problem that you are having, has something to do with the entire cylinder head.

109 k possible jump timing on that bank 3.5 belts last about 105-110k

Check compression, plugs and wires to that side of the engine. Let me know what you find. Also, make sure the fuel pressure regulator is working properly.