I never had much trouble with Killer Prime so I don't remember exactly what team I used for him, but I do have the Prisoner and used him for pretty much all of Night City. Without him, I would probably never have even made it to madness so I sympathize with that dilemma. I can offer some advice though:

•First, I wouldn't bother with Horus or the Madam, as they are both crowd control-based characters and bosses are immune to stun/sleep/etc.

•If you have Iron Eddie, using him along with a purple demon spawn can be a great way to both clear the trash waves and deal some massive damage to KP, since the demon spawn automatically drops crave on enemies in the first turn, and Iron Eddie has a basic move that stuns and places 2-3 silver burns on anyone with crave on them. Still couldn't stun the KP, but a half-dozen burns that knock off 10% max HP each turn will kill anyone quickly (plus crave will absolutely ruin him if he's getting healed a lot).

•The Alchemist is also great against high-health bosses since his power attack hits for almost half the enemies' max health and gives him an extra turn, so it can be used over and over if you have enough power (it only costs 5). Plus his basic cleanses all debuffs on your team which is also great against KP.

•If you have Clansman Eddie and any two allies that can generate lots of fury while still fighting effectively, his fury move can be a real game-changer as it gives your whole team extra turns while also making them immortal.

•Anybody who is able to stack lots of marks is also a great solution to enemies with stupid amounts of health since their damage scales with max HP. Mark talismans on a character who is likely to gain multiple actions in a single turn are especially potent -- Eternity Eddie shenanigans probably being the easiest (albeit least satisfying) way to accomplish this. If you're fortunate enough to have Rainmaker Eddie, you can use his past power ability to double the amount of marks on a target which can result in pretty much an instant kill if you're able to stack several marks with someone else.