Most of the components you mentioned are controlled in part by way of the GEM. Check your grounds, flaky grounds can give you an intermittant problem.
Also a bad ground can cause the alternator to NOT charge the battery. When battery is fully dead, or very low on charge, and if the ground is re-established and the alternator had to recharge it, it may put undue stress on the alternator. IF this occurs repeatedly, it may burn out the alt.
So check your large battery connections, at both cable ends, both pos and neg, and to the starter, and engine block, from the engine to the frame, and the little ones, esp at the left hand side above and below the headlight, any on the firewall, and look for one inside the passenger compartment on or near the firewall.
__________________
BroncoJoe19
2006 Alt Fuel Jeep (electric)
'98 windstar 3.8L
'99 Crown Vic 4.6L
'90 Full Size Bronco 5.0L
I'm not a professional mechanic, take my suggestions with a grain of salt, or a cup of coffee 
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