OK, I must have been getting tired because I didn't reset all the files for that successful test. I was running with the "old" 747-400.xml.
a. The vertical modes of the autopilot are unstable with the "new" (2013205) 747-400.xml file. Replacing with the the "old" version (20130709) restores stability.
b. The autothrottle is broken in the sense that the SPD button on the glareshield panel does not work as it used to and the autopilot dialog doesn't set properties that the autopilot code expects.
When the SPD button is pressed, /autopilot/locks/speed is set to "speed-with-throttle-ias".
When the THR button is pressed, /autopilot/locks/speed is set to "speed-with-pitch-trim"
When the "Speed with Throttle" radio button is selected, /autopilot/locks/speed is set to "speed-with-throttle".
When the "Speed with Pitch" radio button is selected, /autopilot/locks/speed is set to "speed-with-pitch-trim"
The "new" autopilot.xml file has changes at lines 1804 and 1836 that use "speed-with-throttle" to enable auto-throttle instead of "speed-with-throttle-ias". So the SPD button does not enable auto-throttle. On the other hand, all the servo drivers in that file work with "speed-with-throttle-ias" and the autopilot.nas file has lots of if statements that expect "speed-with-throttle-ias", so using the autopilot dialog to set "speed-with-throttle" doesn't work too well.
The simplest short-term solution is to revert those changes at lines 1804 and 1836 in autopilot.xml, changing "speed-with-throttle" back to "speed-with-throttle-ias". The SPD button can then be used to enable auto-throttle.
At least it seems to be flying again and those that want to can look at the new instruments.
ps. Is it just me, or has the texture disappeared from the forward part of the cockpit? I've just got glaring white. Overhead and pedestal are OK.