The heads and the cylinders are off - anything else to take a look at?
 

This is on my 73 FLH. The motor is stock. I had problems with it going completely flat in 4th gear under load. Changed the ignition, timing is good, tried all different combinations of jets on the Super E, good fuel flow, changed most of the parts in the carb. I pulled the heads in case it was a valve problem. Since I had them off, I pulled the cylinders and the pistons. The top end is at a local shop right now to be looked at and redone if necessary. I have all of the oil lines off as I am replacing them since some of them looked pretty bad. Now that it is apart to that extent, should I be checking something else, such as the cam? I never did that before, but I never did any of this other stuff before either, but it's winter and I have the time on the weekends. Thanks. BTW, Happy New Year to everybody.

Well before I chucked the grenade I would have looked at the carb. Did you ever think about checking the float level (maybe not getting enough gas). Also when was the last time you pulled the petcock to ensure that the filter was not blocked.

And have to say that if a fuel filter has been installed between the petcock and carb but installed it in the wrong way, it will cause a flat responhse under a load (there is an arrow on most aftermarket in-line fuel filters that show how it should be installed).

Yes, I checked the float level. Even changed the float and the seat. Pulled and cleaned the petcock screen when I was first starting to diagnose the problem. It also had an in line glass filter. I took that off to see if it made any difference. It didn't.

I also suspect carburation...
The "E" is notoriously rich to go on a 1200.
Bet if you actually put a Carb that got some velocity accross the venturi...it would be much better.
The Bandix is Plenty of Carb for any 1200, and the CV will make it into a Different bike altogether...Happened when I removed an "E" and put on a CV!!!

Edit; I can Guarantee that a Ka-Sneeze [stocker] can be made to run better tha the "E" on a Smaller displacement bike, exception being at WFO

I don't think that I have much else to try after I get the motor back together. I am going to take the E apart now that it is off of the bike and soak it in some carb cleaner. I pretty much already replaced most of the parts in it. If it still does it after that, I'll think about replacing the carb.

Just a side note. Have you thought of using Cometic gaskets? Lots of folks use James. I am very pleased with Cometic so far (1 Pan, 2 Shovels and 1 EVO)

Yes, that is what I have.