You need to make a specially-shaped support for the piston that completely surrounds the pin boss. Then set up precisely straight over the wrist pin with a correctly-sized pin pusher. Usually, the piston is ruined while pressing the pins out of the rods, but the rods shouldn't be damaged at all. I'd suggest finding an automotive machine shop with the right tooling, and pay them a little to remove the pistons the right way. It will cost considerably less than replacing the rod you've already ruined. Heating the small end of the rod is the right way to install the new pistons, but it also takes a jig to get the pin centered properly. Unless you plan on building a lot of engines, paying a pro is the cost-effective way to go for both removal and installation.
Jerry