Here's a short summary of the steps I took to correct my harsh shifting transmission issues.
I bought my 1994 f350 CCLB 4x4 ATS diesel about a month ago with a firm shifting transmission. The seller wasn't the previous owner and had little information or history on it. I use to be a professional automotive mechanic and now an aircraft mechanic, but auto-transmissions are my weak point. I performed the normal new-owner maintenance (oil, filter, lube, tune-up) but the problem remained.
I researched the problem on FTE and studied FORDF250HDXLT notes on the transmission.
I checked for codes on the computer and came up with code-11 (system passed).
I then replaced the TPS sensor and adjusted it to 1.2v and idle and 3.87V WOT. This made the transmission shift even worse since it wouldn't shift til 2500-2800rpm on a normal take-off.
I cleaned the transmission connectors from the solenoid pack to the computer.
I checked the MPLS.
I checked the fuses.
I ohm'ed out the shift solenoids and the Trans-Oil-Temp sensor.
I re-seated the transmission relays.
I checked the grounds.
It seemed like the computer thought the transmission was working correctly. I concluded that the problem must be inside the transmission like a broken spring or stuck valve and not a computer problem. I ordered a digital copy of the E4OD service manual on ebay for the exploded parts diagram only to find out its the same one thats posted on Google for free.

I removed the transmission pan and snapped a few pictures for future reference. I didn't notice it at the time, but there was a piece of sheet metal sandwiched under the accumulator body (just visible at the corners and circled in blue).

I got the accumulator off the truck and on a work bench and pulled it apart. The 1st thing I noticed was it had 4 springs in some of the accumulators where the service manual indicated only 2 were present. This lead me to believe the truck has a shift-kit in it so I researched e4od shift kits online and found the trans-go e4od kit which has 4 springs in the accumulators. I found the instructions to the shift kit where it mentions drilling holes in the "calibration plate" to get a certain shift firmness. I checked my transmission again and found the "calibration plate" still stuck to the gasket. It popped off easily. I found the trans-go logo on the plate so I knew the manufacture of the shift-kit now.

The trans-go instructions list different size holes to drill the "calibration plate" depending on the engine.
The diesel spec list- 2nd gear: 0.110" / 3rd gear: 0.073" / 4th gear: 0.086".
The P/O drilled it to- 2nd gear: 0.175" / 3rd gear: 0.128" / 4th gear: 0.157".
So this was the cause of my hard shifts. Preferably, I would have liked to restore the transmission to stock configuration with the stock springs and stock holes and valves but since I didn't want to pull the transmission and disassemble the pump, the easiest solution was to purchase another trans-go e4od-hd2-d shift kit from Summit for $55 and drill the holes smaller.
In my case, I drilled to the V-8/V-10 specs. 2nd gear: 0.093" / 3rd gear 0.082" / 4th gear 0.093".

I threw the transmission back together and torqued everything to spec, filled it with fluid and drove it around. On the test drive I noticed the shift were still firm, but comfortable. It still had the late shift problem so I backed the TPS sensor to 1.0V at idle. Now the transmission shifts at 2000-2200 and acceleration feels more fluid. 1st to 2nd shift and 2nd to 3rd shift feels good. 3rd to 4th is a little firmer. In hind-site, I wish I would have drilled 4th gear hole to 0.076".
So there you go... My adventure and cure of a hard shifting transmission. I hope this helps someone diagnose and repair their hard shifting transmission.

 

I guess autos aren't your weak point any more!

 

Learn fast, this one does.

 

nice detective work!! nice post.

 

Merry Christmas!

 

wow we've been up to the same things!
"The P/O drilled it to- 2nd gear: 0.175" / 3rd gear: 0.128" / 4th gear: 0.157"."
holy crap.that's off the charts! that must have felt worst than limp mode!
someone didn't research which size bits they needed for something close to reasonable i guess.nice discovery!
i think i would have called transgo directly though and asked them about just buying another plate.or did you try that?

man.thinking about this a bit more.those must have hardly felt like shifts at all.more like just banging into gear.
you know,if those new holes feel really firm even still using the v8/v10 sizes,then it's possible you've a lower than stock stall converter too (which makes the kit installers mistake even worse.)
in my f250, iv got an extra low stall converter.i wonder what he set the thing to in that one.whatever he did,he got it just right in that truck.he probably followed the instructions and went with the 6 cyl in that case.(he installed the full tugger in that truck during reman.)