I just got a 2001 LX470 with the ML non-nav and I'm looking to do the same thing - just replace the head unit and keep the factory ML amp and speakers. I know that replacing the entire system will probably sound better, but the existing system doesn't sound bad to my ears.
I've read all of the threads on doing this, and this seems to be the best thread that addresses a "plug and play" solution. I admire the work so many of you have done on wiring diagrams, but I want to do this myself and my time is limited. And I always under estimate the amount of time involved with these projects. For example, just removing, reconing and replacing the subwoofer took me a whole day (including glue drying time). YouTube makes everything look easy!
So, I'm looking at the Alpine ILX-207 double din unit. i have the bezel off of ebay. For the plug and play aspect, I've read that there are the following options: (1) some have said there is no plug and play option, (2) some have used the the TYTO-01 harness from Crutchfield for about $65, (3) and some have used the BeatSonic SLX-82AAD or SLA-82AAD for about $259, and (4) the Metra 70-8112 harness. The BeatSonic is spec'd to work with the ML system and the TYTO-01 is only spec'd to work with a JBL factory amp. However, the TYTO-01 has been reported to work with the ML amp.
From what I've read, the stock ML amp needs a digital, not an analogue 12v signal to turn on. My guess is that is the boxes in the TYTO-01 and BeatSonic harnesses make that conversion and send the correct signal. The Metra harness doesn't seem to have that capability.
So, I'm leaning toward getting the either the TYTO-01 harness or the BeatSonic harness. It would be great if the TYTO-01 works, but I am concerned about reports of noise in the system. While it's more expensive, the BeatSonic seems like it has the best chance of success for a simple, clean low-noise replacement. Am I right on this?