zergl

Did you upgrade your tracking station to level 2 in your test save? Some of the autopilot features are apparently hardcoded to need an upgraded Tracking station (for obvious reasons as they work with maneuver nodes) which I doubt you can change on your side. Somewhat bad behaviour on MJ2's part though for not being explicit in the individual module prerequisites.

I pretty much figured out the problem with MechJeb but I'm not familiar enough with ModuleManager to fix it. The culprits are the method UnlockCheck() in ComputerModule.cs and this section in the part.cfg of the pod and AR202 modules: MODULE { name = MechJebCore MechJebLocalSettings { MechJebModuleCustomWindowEditor { unlockTechs = flightControl } MechJebModuleSmartASS { unlockTechs = flightControl } MechJebModuleManeuverPlanner { unlockTechs = advFlightControl } MechJebModuleNodeEditor { unlockTechs = advFlightControl } MechJebModuleTranslatron { unlockTechs = advFlightControl } MechJebModuleWarpHelper { unlockTechs = advFlightControl } MechJebModuleAttitudeAdjustment { unlockTechs = advFlightControl } MechJebModuleThrustWindow { unlockTechs = advFlightControl } MechJebModuleRCSBalancerWindow { unlockTechs = advFlightControl } MechJebModuleRoverWindow { unlockTechs = fieldScience } MechJebModuleAscentGuidance { unlockTechs = unmannedTech } MechJebModuleLandingGuidance { unlockTechs = unmannedTech } MechJebModuleSpaceplaneGuidance { unlockTechs = unmannedTech } MechJebModuleDockingGuidance { unlockTechs = advUnmanned } MechJebModuleRendezvousAutopilotWindow { unlockTechs = advUnmanned } MechJebModuleRendezvousGuidance { unlockTechs = advUnmanned } } } What it does is it checks for both the part and the unlocked tech node for some reason while only the part's requirement gets changed but the requirement for the unlocked tech node (as defined in the above snippet) does not. Changing the instances of advUnmanned to advMetalWorks and unmannedTech to advLanding directly in my MJ2 part.cfg files fixed the missing options for me.