Not entirely sure how the thread got so side tracked...
In any case, in my personal and professional opinion of the "dealership incident" is as follows:
-Customer was aware that warranty may be denied and was okay with this
-Technician basically refused to work on the vehicle
-Customer was still expected to cover cost of diagnosis, even though technician refused to work on the vehicle.
The last part is the issue I took with the technician & service writer, I have no problem if the technician wants to back out of the issue or even if he wants to half-ass it and just blame it on the aftermarket stuff and call it a day. Its when the technician and/or service writer expect to get paid for not doing anything that upset me. The issues was that the technician didn't do anything beyond pop the hood and see the aftermarket wiring. Had he at least said, "I checked for DTCs and some of them are related to Voltage supply issues and I am suspecting the alternator is at play here and I want to restore the system to stock to verify" I'm sure the OP would not have had an issue, where as the way it was presented was basically refusing to work on the vehicle but still wanting to take the money for a job they didn't actually do.
[MENTION=68685]Ducmonsta[/MENTION] is right, we (as technicians) are getting not paid to diagnose your vehicle completely. What we are getting paid for is a .8-1.0hrs of labor to perform diagnostic tesing. I have come across jobs where I have to go back and ask for additional hours because we're struggling with diagnostics and/or the issue is so big we can't just figure it out in such a short amount of time. But that is on the service writer to present the job as "we are charging you 1hr to START diagnostics, if we need additional time it will be up to you to decide how much further you want to go." This is designed to help us avoid cases where the customer gets a bill for 20hrs of diagnostics when they only expected 1-2hrs.
The dealership has the right to refuse service to anyone for any reason, the same as most any other business. Now its not in their best interest to do so, but we've had to turn away some customers before. I had a lady who had something seriously wrong with her head, because the Prius she drove was a biological hazard on wheels! The seat frames were flaking rust from god knows what she pissed/spilled in the vehicle and the stench and filth was so severe we put on hazardous particulate filters, gloves and taped seat covers on our uniform to work in that vehicle just to program a key. Afterwards we ask the customer to not expect us to service that vehicle again.
The issue with warranty pay is that the dealership pays upfront for any warranty work, then Toyota reviews the warranty repair orders and authorizes reimbursement. Which means if we charge 3hours of diagnostics under warranty and Toyota comes in and says, "customer had an aftermarket alternator, issue is electrical, warranty is voided." The dealership is stuck with the bill, so many dealerships will nip a job that even hints it could be voided in the bud to avoid any possible conflict (hence why so warranty is such a pain in the ass for members likes us.)
Post Note-
[MENTION=83083]rigtec[/MENTION]
What mods exactly have you installed on the vehicle and does the vehicle have any extras from when you bought it? i.e. dealer/port installed alarm, ect?
I don't remember if I asked you before or not. I'm trying to get an idea if the alternator may be worth focusing on, the issue is that IF the alternator is charging within the ideal voltage ranges it shouldn't be an issue. Most modules are running some form of actively converter to reduce the voltage to a stabilized 5v; otherwise when the alternator jumps from 13.4-14+ volts the 5v reference would always be in accurate. The issue though is that if grounds or powers INTO those modules is wonky that could skew some things.
More importantly we still need an idea of the DTCs you have in the vehicle to get a more accurate idea what section of the electrical system we need to address. If the CAN bus was affected it'd take down the entire network depending on the issue (short to power or ground would take down the network lines due to failsafes), where if it was a break or even weird signalling/excessive resistance it could cause issues to/from a particular module. At this point we're still flying blind without the DTCs and/or healthcheck report to get an idea of what is going on.