The gaskets should be bonded on the separator plate. They were on my 99 Ex.
Udate! First off, the gaskets are bonded to the separator plate.
Next, some background. My truck has 140000 km on it. I have changed the transmission fluid every 2-3 years in the past. For the last six months or so, my transmission had been shifting "funny". The shifts were often soft and late. I thought I might have had the 2-3 shift flare a few times. The fluid level was correct and had been changed approximately 25000 km earlier. The tranny seemed to be basically shifting inconsistently. Nothing horrendous mind you, it just didnt' seem to be "quite right". I decided that a fluid change and valve body rebuild was in order after reading the numerous threads posted on this site.
I did the valve body rebuild three days ago. The parts that I installed were;
- the Ford TSB kit,
- the new separator plate,
- the updated solenoid bracket,
- a new EPC solenoid,
- and of course new filter and fluid. (I needed 8 liters to top up my tranny)
Once I had everything apart, I discovered my old separator plate gasket had blown right beside the reverse servo. It looked identical to Kaiser's picture as posted on page 6 of the Diary.
The valve body, solenoids, and pan were generally quite clean. I didn't find any other obvious problems.
I followed the directions in the stairway to the diary and the diary itself as closely as possible. I'm happy to report that everything went very smoothly!

Excellent instructions guys!!!
The only thing I would add to the instructions is more emphasis that you need a BIIIIIIGGGG drip pan. I bought the biggest drain pan that I could find, but it still wasn't big enough to catch all of the drips. Big_billys idea of using a 50 gallon drum bottom would be ideal.
The final verdict is.....Success!!! My transmission now shifts smoothly and consistently!!!

Once again, a big THANK YOU to everyone who has posted instructions/information on how to do this job!!!