I did some extensive research on the PA. Here are my suggestions:
As to units I say the standard infantry unit should be the PA Enforcers and have the PA logo on them somewhere and be about the level of Zsinj's Raptor Troopers as elite troops.
Replace the regular Stormies role with Imperial Army Troopers
http://starwars.wikia.com/wiki/Imperial_Army_trooper(you could use the Navett model minus the rank and hat, place the long black helmet on their head like the NR troopers used to wear or use the old field commander model with different coloring.)
The Inquisitors(as generic Dark Jedi opposed to the NRs Jedi) and their Judgement Troopers as Zsinj suggested.
The Enforcement Picket Ship and multiple ships used by corporate powers(marauders, corvettes and some pirate like vessels.
Also to further distance from the IR counterpart, I suggest leaving the coloration on the Hulls of their ships as when they were a warlord faction(I.e the light blue stripe along the edges of the ISDs and VSDs. Putting the colors or logo on the ground forces too would help to differentiate as a breakaway faction.
The Floating fortress as a heavy command vehicle.
Also you could deny them certain IR ships. For instance the PA might not construct Tectors, SSDs, or TIE Defenders.
For heroes I've got a few suggestions as well:
Grand Admiral Octavian Grant who took refuge in the PA for 2 yrs, the cause of his defection was loss of faith in Kaine becoming the dominant force in the galaxy. He could have an ISD. TO acquire him you have to do a mission to save him from IR forces trying to kill him. If successful he joins you as a hero.
Gov. Ib Dekeet as an Imperial Gov. he was part of the PA talks and brought considerable land forces into the PA. He could have a ground command vehicle and be the land hero besides Jerec.
http://starwars.wikia.com/wiki/Ib_DekeetGregor Raquoran was Commerce Master Commissioner and aligned with the PA in the PA talks. he brought considerable financial power to the PA. A shuttle in space and gives a monetary boost to the planet he is on.
http://starwars.wikia.com/wiki/Gregor_RaquoranElta Besk was the head of Dynamic Automata, a droid design and manufacturing corporation. She joined the PA because it was more lenient on slave labor than the NR. She could offer a production boost in build time being reduced. She could have a shuttle in space.
http://starwars.wikia.com/wiki/Elta_BeskWyrn Otro worked for Galentro Heavy Works corporation, also testing many of the weapons manufactered. He could also have a ground command vehicle and he could give an attack boost to heavy vehicles in the Alignment.
http://starwars.wikia.com/wiki/Wyrn_Otro