when rebuilding, replace ALL seals. Your wasting your time if you don't
With the calipers still bolted together, drain all the fluids you can from it. Then used compressed air to help push the pistons out. Clean the pistons really good so there is no gunk left on them. clean up the caliper bodies really well, paying attention to where the pistons go.
Don't use marring tool on the pistons when trying to remove them.
As for the alignment of the front wheel, just cause the wheel spins freely without the calipers doesn't mean the forks are straight. Make sure that axle slides into the forks/wheel without binding, and withouth the use of a mallot, or other tool to drive it in. Honeslty, that axel should just slide right in with no issues.
You may also want to check the master cylinder to make sure it's working properly. It's a two way valve basically. Pull the lever and it pushes fluid into the lines. Let the lever off, and it releases pressure in the lines. if it's not working on the release part then your calipers could bind on the discs.
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Charles Gallant