Paul and Mike
I don't know what manual you are using on the Hydro but I have both the IH manual and one from Sauer/Sundstrand for the 15 series U type hydro. The IH manual mentions that some swash plates are drilled all the way through and to be careful not to drive the pins through the shaft and into the lower holes in the swash plate, they also only mention one pin on either side. Every swash plate I have seen is drilled all the way through, and every hydro I have seen has two pins on the side of the trunion bracket.
The Sauer/Sundstrand manual has different directions and this is the way I always do it. It helps if you build the wood stand for holding the hydro and then mark it like this.
Place the hydro housing on the stand like the picture, rotate the swash plate to its full forward position like the marker drawing on the stand. With a 3/16 dia punch drive the pins through the shaft until they touch the housing (Remember there will probably be two pins on the trunion bracket side and only one on the control shaft side.) when the pins contact the housing you should be able to rotate the swash plate back the other way and the pins will drop into the housing. Tilt the swash plate back to its full forward and drive out the other pin on the trunion bracket side. You should then be able to remove both shafts.
On some swash plates the rotation forward is 15 degrees and only 7 1/2 degrees reverse so be sure you are rotated in the forward position or you will be in trouble.
Here is another picture of the inside of the hydro with the swash plate removed and you can see there is more space to remove the pins when you are rotated CCW or the forward position on the hydro shaft.
Note I marked the stand with the swash plate rotation for pin removal and which side has the single pin and the side with two pins. Also the marker drawing on the top indicates which side of the hydro pump has the flat side so when I put it back together I don't install in wrong.
One last suggestion, the manual tells you when you re-install the shafts to line them up and then drive the pins through the swash plate into the shafts. If you do it that way the shaft normally moves and you have a heck of a time trying to get the pins in, I have what I think is a better way.
I drive the two pins into the shafts before I put them into the swash plate, then look down in the holes in the swash plate and when they are lined up with the pins in the shaft I use the 3/16 punch and drive them into the lower hole in the swash plate.
On the side with the two pins, once you have the first pin started install the second pin and drive it in. Make a mark on the punch 1/4 inch from the end and drive the pins in to that mark, which will center both pins in the swash plate and the shaft.
On the side with only one pin, measure the length of the pin, install the punch in the hole and add 1/2 of the length of the pin and mark the punch, when you drive the pin in it will be half in the shaft and half in the swash plate.
This way is much easier than the way the book tells you to do it as far as I'm concerned.