Joe, as I recently did both front calipers, rotors and stainless lines I'll try to help. First, I tried the rebuild myself on the second caliper, before I had the manuals, and wasted a good deal of time, thinking I had it right til I loaded the pads and the piston seals popped out! Another rebuilt caliper coming up!!
Manual does give some worthwhile tips. Pistons are easily pushed out using compressed air, applied via inlet, being careful to "catch" them against a piece of wood to prevent projectile damage, and not use excessive pressure. If you use pliers it's almost inevitible that damage will result.
Clean the caliper thoroughly using brake fluid in the cylinders. Apply a coat of brake fluid to the piston seal and fit it into the groove in the cylinder wall. Apply a coat of BF to the entire inner surface of the cyl and outer surface of the piston. Apply a coat of specified grease (rubber grease or niglube RX-2) to the boot and fit in the groove on ends of cylinder and install piston boot onto caliper body. Now insert piston into boot and cylinder. Don't force piston into cylinder. Now position boot in grooves on cul and piston. Sounds easy!??? Best of luck. Think I might have been successful with the correct assembly order.
Glenn