It will be interesting to see if the cat is causing the problem. Though it could also be a sticking EGR valve. I know you said you cleaned the valve, but I've never been able to successfully clean an EGR valve.
One indicator of a sticky EGR is that everything works fine, but it might stall at the end of the ramp coming off the freeway. You hit the key and it fires right back up and off you go. Or it might sometimes idle very rough at the end of the ramp, and at other times it idles smooth at the end of the ramp. If idling rough take a small hammer and tap on the EGR and see if the idle smooths out. If it smooths out replace the valve.
On the timing front it is possibly that the timing is not advancing and retarding as it should. First thing I would do is point a timing light at the engine and see if the timing mark is dancing around at idle which it should be. Then give a few rev's while watching the mark and make sure the timing advances and returns back to where you saw it at idle. I know this was mentioned above, but at this point the timing mark should NOT be at 10 btdc or whatever the actual spec is.
Now find the SPOUT connector (a two wire harness plug with a jumper plugged into it) which according to the link from enblethen it looks like could be under the brake booster (it could also be right next to the distributor). Unplug the SPOUT connector and check the timing. With the SPOUT disconnected the timing mark should be where you set it during the engine install and it should not be dancing around too much.
