1995 Jeep 4.0 misfire at idle

I have a 1995 Jeep 4.0 that has a misfire at idle.  This is a new motor and seems to run fine once off idle.  Exhaust at idle has an obnoxious smell like its rich but with some other chemicals in the gas...not a normal rich exhaust smell.  I have smoke tested both intake and exhaust and I believe fixed all vacuum and exhaust leaks.  I have scoped the following: 

CKP with CMP;  - looks like its in sync to me

#1 injector driver at ECM with CKP; 

coil control signal at ECM with CKP;  - coil spark lines do not all rise up or are inconsistent in height

coil control signal at ECM with #1 injector driver at ECM; -  coil spark lines do not all rise up or are inconsistent in height

#1 injector driver at ECM with clamp on coil wire to distributor;  - This one doesn't look right but I have no idea what might be happening - coil pattern has kind of a wave to it

#1 injector wire at ECM with clamp on #1 spark plug wire.  - this ignition pattern is inconsistent also...doesn't seem to be firing consistently

other notes:  1) Pulled wire off coil tower and turned motor over with a probe light near coil post - spark jumps about 3/4"   2) put an inline spark tester on each plug wire and let idle... all cylinders similar .... spark light is bright and consistent until misfire then light dims (all cylinders did this).  3) put inline spart tester on coil lead to distributer and let idle......light very bright and could not see any dimming with misfire.  4) I mentioned this is a new motor... but the motor had the same misfire at idle before the rebuild.  5) fuel pressure is a consistent 40 psi

All of this seems to point at some issue with distributor to me????  its a new distributer.... but I did have to re-clock the cam gear 180 deg to get the CKP and CMP to sync correctly...

Any help is very much appreciated.... I have been struggling with this for a while now.

Any thoughts on what is causing the wave pattern in secondary ignition in last picture?

That wave is not, really, there. You can try moving your secondary probe closer to the coil. A primary voltage waveform of the ignition coil would produce a truer waveform.

It looks like your scope and secondary probe might not have a good ground connection.
You should, also, increase the sample rate of the scope to, at least, 1ms/s.

With a missing cylinder at idle only you may deal with a leaking valve. I'd run a leak down test, be the engine "new" or not.