Actually, you can do it with less. The only file you need to replace is [unpacked pbo root]\scripts\VAS\functions\fn_fetchCfg.sqf
Just replace it with one from the unedited VAS code.
This was an easier fix than I expected, actually (a testament to roy's well written and laid out code, too)
For anyone with this issue, go to the file [modroot]\fnc\respawn\fn_onkilled.sqf
Find the lines
if(_isCrew) then {[player] call PO3_fnc_setAsCrewman;};
if(_isPilot) then {[player] call PO3_fnc_setAsPilot;};
They're at line number 50 and 51. Right below them, before anything else add this:
player enableFatigue PO3_param_player_fatigue;
That will fix the problem right up.