Speaking from recent experience (I just did mine 2 weeks ago), here's what I ran into.
First, although they say not to separate the halves, I don't see how anyone could thoroughly clean the bores without doing this.
Mark the caliper halves and when you remove the pistons, mark them too. I used a numbered stamp set. You can mark the bottom of each piston and it will have no effect on performance as it's not a sealing surface. *** BEFORE *** pulling out the pistons, make note of their position in the caliper bore. There is a recess in the top of the piston. All the book says is it should point toward the bleeder screw. I was able to blow my pistons out of the bore with an air tank and 40 psi pressure. Less than that seemed like it wouldn't get them all the way out. Also, I popped the pistons out before I separated the caliper halves. Less holes to try to plug this way.
I pulled mine apart and there was all kinds of crude in the bottom of the bore. Cleaned everything really well using mineral spirits first, then Brake Clean to remove the mineral spirits. Didn't need to hone them.
Inspect the pistons really well. I had one piston that had some surface roughness due to sitting in the crude. Went to the local brake parts warehouse here in town. Of course, they didn't even list the pistons in their books, it was too old. But, they looked at mine and said it was ok, just to clean it up with emery cloth and reassemble. Trust me, Don't listen to the "experts" and don't do it. Buy a new piston if you need too. When I tried to put the piston back into the bore, it tore the seal. So, ordered another rebuild kit and this time a new piston.
When reassembling, lubricate EVERYTHING very liberally with clean brake fluid. Put the pressure seal in the bore, then the dust seal. I don't know if it matters when you put the metal dust seal cap into place. I did mine before inserting the piston. Didn't seem to matter. Mount the piston half in a vice by the mounting ears, start the piston by hand and use a 6" (minimum) C Clamp to push the piston back into be bore.
The piston may tend to "cock" in the bore slightly. Don't force it, you'll tear the seal (don't ask how I know this please). Reposition the C Clamp to even out the piston. It's important that the piston go in evenly.
It takes quite a bit of force for the piston to clear the pressure seal. When it does, you'll feel it. Then, the piston compresses real easy, just like doing a normal brake job.
Reassemble the caliper halves, replacing the O-ring that goes between them. I noticed there was some form of loctite on the bolts when I took them apart. I cleaned the threads using a wire wheel. Then I used Red (high heat) Loctite on the bolts. I couldn't find a torque spec on the bolts, so I "guesstimated" and torqued mine to 40 ft lbs.
Hope this helps you a bit. Best of luck.