The fluid behind the piston may be making it hard to push the piston into the bore.
If you crack open the bleed valve on the slave cylinder, if may relieve any pressure and allow you insert the piston. Do NOT allow brake fluid to contact paint as it will damage it.
Connect a hose or cover it with a cloth to keep fluid from squirting out.
If you're able to insert the piston, push it all the way in until seated, then tighten the bleed valve and gently pump the lever enough to add fluid into the cylinder (watch your master cylinder level).
Of course don't pump enough to push the piston out, but just enough to fill the cylinder slightly.
Then open the bleed valve and push the piston in until it seats then close the bleed valve. This may push out as much air as possible.
Reattach the combined slave cylinder/side cover, and then bleed the system until no air is remaining.
A Mity-Vac kit would come in handy about this time. But the traditional way should work as well.
This is similar if you had your calipers completely disassembled. Just more pistons to deal with.