I generally start off like that myself with no faction behind me so it is not that. I do not use UAF so I am unsure if that mod had anything to do with it, are they pirate aligned? When you state they have a large scale territory I am confused since they start off with 1 system, what size sector did you generate and how much of it was owned by JYD?
They start off as neutral to the Hedgemony and in my experience the Hedgemony outguns them in my games.
Well Nexerelin does love to toss monkeywrenches into the mix that is for sure. You may have had numerous random faction relation adjustments (like weddings and such) not go your way.
Well that is your call of course, if you do I would certainly like to hear about it.
Now that you mention that, what mods are you using? I ask because maybe you are using something I am not, though I do run a very mdoded game. If you are unsure how to do that, go to your starsector folder then to the mods folder and in that folder is a file called enabled_mods.json is a list, here's mine:
Spoiler
"all_the_domain_drones+NewDrones",
"AngryPeriphery",
"ARSWP",
"Cryo_but_better",
"apex_design",
"lw_autosave",
"timid_admins",
"BSC","bc",
"HMI_brighton",
"ORK",
"CJHM",
"Csp",
"combatactivators",
"chatter",
"cmutils",
"timid_commissioned_hull_mods",
"lw_console",
"Toaster_deciv",
"diableavionics",
"Diktat Enhancement",
"dex",
"edshipyard",
"EmergentThreats_Vice",
"EmergentThreats_IX_Revival",
"Everybody loves KoC",
"FPE",
"GrandColonies",
"GMDA",
"HMI_SV",
"hte",
"HIVER",
"aerialcombatsuit",
"IndEvo",
"Imperium",
"timid_xiv",
"JYD",
"keruvim_shipyards",
"lost_sector",
"lw_lazylib",
"LLI",
"luddenhance",
"lunalib",
"exshippack",
"MagicLib",
"Marvelous-Personas",
"Mayasuran Navy",
"MoreBarMissions",
"MoreMilitaryMissions",
"ness_saw",
"wisp_NeutrinoDetectorMkII",
"sun_new_beginnings",
"nexerelin",
"sun_nomadic_survival",
"objects_analysis",
"ObviousNeutron",
"JYDR",
"PirateMiniMegaMod",
"pearson_exotronics",
"wisp_perseanchronicles",
"portrait_changer",
"progressiveSMods",
"pt_qolpack",
"assortment_of_things",
"refitfilters",
"RetroLib",
"RetrofittedBridge",
"roider",
"rotcesrats",
"ryaz",
"sun_ruthless_sector",
"Scrapyard",
"SCY",
"second_in_command",
"secretsofthefrontier",
"SEEKER","shadow_ships",
"swp",
"spacetruckin",
"speedUp",
"sun_starship_legends",
"StopGapMeasures3",
"timid_supply_forging",
"supportships",
"surveycorpssp",
"tahlan",
"presmattdamon_takenoprisoners",
"terraformingmadeeasy",
"exalted",
"metelson_release",
"star_federation",
"timid_tmi",
"TORCHSHIPS",
"TTE",
"TTSC",
"underworld",
"US",
"unthemedweapons",
"vic",
"TouchOfVanilla_vri",
"whichmod",
"XhanEmpire",
"audio_plus",
"prvagni",
"prvextra",
"prvlib",
"prvPath",
"prvrb",
"prv",
"shaderLib",
"yrutl",
"CFT",
"HMI",
"pantera_ANewLevel30",
"vayramerged",
"starlords",
"eluxor_hegtales",
"Shmo_ICFB",
"missingmidlineships",
"missingshipspirate",
"QualityCaptains",
"A_S-F","armaa"]