Everything's fine. Apparently, fuses were replaced and the Z1 fired right up. The installer took responsibility and my guess is that the wires should have been secured better. He said sliding the unit in and out should not cause a short, which it didn't. The unit ran fine for two days after I slipped it back in after painting the trim.
Also, according to the installer, the brake light connector was pinched when he reinstalled the instrument cluster. Tracking it down, he said he also found a resistor (or diode, I forget which) on the GS400 emergency brake, which he removed. He said that was causing the brake circuit to appear as if it were grounded, which it was not.
After that, he decided to retrace everything -- and I guess making sure there was more than electrical tape securing the wires. In the process, he found a diode (or maybe it was a resistor) in-line on the GS400's VSS line. He said that prevented two-way communication to send the pulse info to the Z1. Important stuff here because he removed it and the Z1 finally is running 3D hybrid tracking with dead reckoning.
Also, he fixed the rear brake connector, which finally works now. :D
So, there were several fundamental wiring issues, in addition to whatever caused the fuses to blow. It was the first Z1 this installer had done, and he doesn't see as many GS400s as he does F150s.
But I have to say CC did the right thing and that's why I paid retail to have them handle it rather than trying to do it myself. And, hey Pioneer, no quibbling from them about it. It's a $2,300 unit and they wanted me happy.
I probably shouldn't say this, but maybe there's a lesson here for Pioneer. Instead of posting here and raising doubts about what CC might or might not do -- with no first-hand information, I might add -- why not a simple PM with a word of support or encouragement to a customer who is excited about your product and spending a bundle with you? Or at least attempt to get more information before speculating publicly.
At the very least, you should be giving the people in the field enough support as they try to install your new, top-of-the-line equipment on every vehicle manufactured. I've seen lots of questions about VSS and similar problems here and you are obviously following some of the dialogue. But I've seen nothing offered by you to solve a problem. The installer told me his documentation on the Lexus was all wrong, and we found the VSS line from a posting on Club Lexus. Has Pioneer set up as much as a BBS for installers to exchange this info behind the scenes? Maybe so, and if so, fine.
Word of mouth sells the high-end stuff and with the Internet, word travels fast.