I do not know how to upload a save here, sorry.

Got the quest from Angel to help Maria. Got her out of there stealthily-like but when i delivered her to Angel, he gave me the jacket instead of the deed, no problem there, and he left. Maria did stay there though but without being recruitable, i used Lynx to talk to Angel. I reloaded the save and this time i used Cougar to talk, i think he is the one that initiated the quest in the first place. Angel spoke his lines, gave the jacket, told me about Kingpin's money and took off. Maria joined my squad automatically.

I did try reloading the Pacos-Manuel phase but i don't remember who spoke to Manuel in the first place to initiate the quest. Maybe i need to use that same person to bring Pacos back.

What happens if the Manuel-Pacos quest remains unfinished ? Is Manuel supposed to go get a surgery and then join my little army ? That would make the quest completion worthy.

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You will only miss the chance to get a loyalty bonus in Salinas which is useful especially at the beginning of the game if you are not bringing back Pacos to Manuel and finish this quest.
Nice idea nevertheless, but Manuel already appears in v1.13, UB and several other mods as recruitable character and Vengeance: Reloaded Mod is a sequel to JA2 vanilla story and we in VR team wanted to avoid the repeats of too many trusted story elements and characters and give this mod (sequel) something special.

Apart from that Manuel can not be operated in Arulco and you are doing a good deed for Manuel and Pacos' family. ;-)