Another thought I had. I was told it is easier to check that type of thing with the trans out and upside down. I know nothing about transmissions so I'm going of of others inputs.

 

That is true. In a 4L80-E the depressions the checkballs sit in are in the case and above the separator plate. Dropping the plate without all the checkballs going everywhere is takes steady hands. They will be just sitting in their seats in the plate. (In a 4L60-E all the checkballs except one are in depressions in the valvebody and below the separator plate.) Reinstallation in an 80 is not too bad because you can use little gobs of Vaseline to hold them in place. That works as long as the valvebody is lifted straight into place without shifting around. Installing two temporary studs into the case bolt holes helps with alignment.

 

It may be a while before I can log some WOT info because I burnt a piston and have a new engine on the way and winter weather here reduces the road conditions when doing WOT runs are safe(r). On my trans the WOT shift rpm is set to 5600 for all gears; the ETC RPM Limit vs Gear is set to 5900 rpm and the Fuel cutoff is set to 6000 rpm. My shift speeds are all pretty much stock and don't seem to affect anything and are all well below my actual shift speeds. I have never tried to fix it, but in my logs my 1 -> 2 shifts are generally in the 5100 to 5200 range. My new engine is going to have a little larger Cam in it so I will likely want to figure out why my 1 -> 2 shift is so low. Looks like my problem on the 1 -> 2 shift is just the opposite of yours. I read somewhere to set your RPM limits 500 rpm above your commanded shift rpm.