Hi Joel, Looks like we are getting somewhere with this one.
I had a look at your captures, I'm not familiar at all with in cylinder pressure wave forms but having had a look through i think we can identify that its defiantly a valve issue, please correct me if i am wrong here anyone.

I have reference wave formed the files to see all cylinders on one screen and have labelled them in the notes. Cyl numbering is 1,2,3,4 from left to Right as you are sitting on the bike.
I suspect, looking at the dips in the waveform at the end of the compression cycle the 2 problem cylinders seem to dip further into negative pressure and hold there for longer after TDC which i would say indicates not a clean valve closing event.
I also labelled in the notes some approximate values for where i think the valve closes/cylinder seals after the tdc event, which i did using the degree cursers and rulers. This shows that the 2 problem cylinders both have more crankshaft degrees before the cylinder pressure equalizes, also the closing event is not as clean a shut of as can be found in the 2 good cylinders.
If anyone with more experience can add anything to this please do as this is my first time with this type of waveform.
Good work Joel,

some nice captures. I look forward to hearing what you find when you pull the top off and have a look.