Didn't read through all 3 pages. I'm just gonna chime in.
1. Any kind of FI on your engine would likely get your warranty claim denied. It doesn't "void" it, in fact nothing "voids" your warranty. Warranty just doesn't cover damage caused by aftermarket components.
2. It's impossible to install the front cover upside down. The front cover covers the cam sprockets which control the VVT.
3. Tuners absolutely change ignition timing to make power. Not so much the Variable Vale Timing. Mechanics can observe the advancement percentange from each cam sensor and compare to another vehicle operating under the same condition to determine if the VVT is altered. Which is very unlikely since your engine does not run. An easy way to tell if an ECM had been modified is by checking the CID. If the ECM is confirmed altered, they can and often do deny any engine repair.
4. Sounds like the service manager is just trying to tell you that they won't be fixing it under warranty. He doesn't necessarily know exactly what had happened, all he knows is that the car was once turboed and tuned. I'm very surprised that Toyota had you remove the mods for diagnostic.
IMHO, your engine is not covered. You run the risk of damaging your engine when you modify it, it's not fair to have someone else pay for your consequences. Now bite the bullet and build one that can take the turbo!
