09 certified electrical issue help

Hi All,
I recently purcashed a 09 tacoma 2.7 liter 4x4(27k) and have driven it 3000 miles and owned it just over thirty days.
Well anyway the other day the charging light came on and just a few days after that the charge system light went to solid Red.
So I figure on the way to the airport I would drop it off at a dealer which was close to the stop were I catch the bus to the airport.

A few days later the Dealer calls me and tells me that the wiring to the alternator is fried along with the fuse box.
They go on to say that they need to bring in a specialist to examine the problem.
2 days after that they call and let me know that they called toyota care, cause I bought the Platnium care protection.
They go on to say that they cannot find the reason that the wiring burned up and that they will replace burnt wires and cracked/burnt fusebox. they want me to pay 225 for troubleshooting/diagnostics and toyota care will pay for parts and labor.
The service rep went on to say that they suggested new wiring harness, however toyota care wants the cheap fix for now to get me back on the road with my truck.
Well I freaked out on them because I feel like I might have gotten burned getting this truck from another dealer. The reason why is when I bought the truck the radio and dash area were disassembled. And at that time the sales guy told me they were removing non-oem stuff like alarm system etc.
This makes me not want this particual truck.
Now looking back I think they were chasing down a short! I'm starting realize that taking dash apart is not needed for modern alarm systems, am I thinking right about this?
So the dealer where the truck is stats that if I have the problem again that they will get into it further.
I'm just bumbed cause I did not buy a new truck to have it in the shop over and over.
The dealer working on the truck seems genuine with how they are treating me, however the dealer I purchased it from still has not called me back and when I spoke with them they acted like they did not trust these techs and wanted me to bring it to them. and went on to say when I told them I don't want this truck anymore they said they no longer had interest in the truck. it was between me and TFS.
Is this how I'm supposed to be treated. I'm about to call TFS myself and the dealer to go ahead with patch/repar. cause I need a vechicle.
Being they cant find why the wiring is burning up I'm bummed and feel it's going to be a reacuring problem.
any suggestions or things need to know about?

 

Couple suggestions,

First Document EVERYTHING.

Now do you have any documentation from your original purchase stating to the fact of the "removal of non-OEM equipment)? If so make copies and provide them to toyota care, and the dealership working on it to aid them finding the problem and also so they can assist in dealing with the other dealership.

Best of Luck to you man, I wish you the best of luck!

 

Got my truck back.
Freeman toyota and service agent Twan are great. did the best they could under circumstance.
if problem persist i'll get another truck.
the truck actually runs better to my surprise. not sure why?

 

What all got replaced exactly?

 

fuse panel cover
wiring to alternator
and that is it. the dealer wanted to replace the harness however toyota care did want to do that yet.
and they never found what caused it.