2007 v6 cooling fans/electric windows causing engine stumble

Hello anybody who can help. My 2007 mustang v6 base model recently had a problem with the Crankshaft Position Sensor and was fixed. All seemed to be fine until the next time I drove it when I noticed that the engine would stumble at idle when the cooling fans would kick on. It is a short stumble and recovers right away but is very noticeable. The RPM's seem to drop just enough to move the needle but then returns to normal. The other day, I also noticed that when the automatic electric windows come to a full-up position, it causes the same motor stumble. First thought is a large load on the electrical system, but the battery and alternator were replaced less than two months ago. Any suggestions would be great!!!!

My original thought was the alternator......my dumb*@# took it to Ford and they replaced it.($800 later). I also read a few places that it was a good idea to go with the bigger battery (40r) rather than the original (96r) so today I replaced that as well. Now I have an added problem. When I changed out batteries, it reset the KAM and had to re-find the idle. I have read many posts with a procedure to fix this and I completed the procedure. When I took it for a drive, It went into limp mode and now shows a wrench light on the instrument cluster. I am told that this is an issue with my throttle body, but it is brand new as well. After a few more drives, the light went away but I just cannot get this car to idle properly. It is just a bit rough and a little low by maybe 50-100 RPM's. Short of having the equipment at a dealership, I have tried just about everything with many different scan tools but cannot seem to find the problem. I wish it would be nice to me and throw a code of some sorts!!!!! I am ready to give up all together.

Has anybody had an experience of Ford putting in a bad alternator?? Is there a test I can perform to check it? Perhaps a voltage leak test on the alternator? I have my doubts that a new part would fail straight from the Stealership but I have seen some weird stuff happen under the hood before.