I've been looking around, and it seems like the best info still online about Neil Young's rig is the gearpage thread I linked to already by the guy who built his own Neil Young rig, whizzer and all, and the 1992 Guitar Player Mag interview of Larry Cragg (Neil Young's guitar tech):
The main things are:
1. He uses more than just the Deluxe amp:
"I have fans pumping a lot of air into the back of the Deluxe, since we rebiased the amp to use 6L6s. We have the speaker there, plus the extension speaker output, which has been significantly padded down with a volume knob. The signal then goes into Magnatone 280 stereo vibrato — the Lonnie Mack amp — with two 12s."
"Neil has his own private P.A. and a Yamaha mixer. He has a separate microphone that's not connected to the house for each amp, and he can mix these to any level he wants. He mainly hears Deluxe, a lot of Baldwin, and very little Magnatone. Out front and on record, you can hear mostly Deluxe and Magnatone."
2. The Whizzer does a lot:
"Here are Neil's Whizzer settings: For the highest volume, we have both the tone and the main volume on 12 and the second volume knob is at about 9.9. When it's really compressed and breathing and screaming, that's whats going on. You can hear it on "Cortez". If we push it past 9.9 the sound goes away. The next button down moves his volume to 10, which just cleans it up. It's still broken up but its less garbled. The third button sets his volume on 6 with that other volume still at 9.9 and the tone just down a little. The fourth preset moves one volume to 3, the other volume to 0, and backs the tone off a bit, its really bright and clean, almost country sounding."
3. FX - The same foot-switch assembly that changes Whizzer presets also switches his effects. Though he does use quite a few different effects in specific songs (an octave down pedal seems to be used quite often, for example), the main ones that are almost always on are his Fender outboard reverb unit and the Echoplex:
"The first thing the signal always sees is the input of a Fender reverb unit. The reverb pan is not in the unit; its usually underneath the stage. This one happens to be more susceptible to vibration than other pans, but it has the tone he likes. He can tell when I try to substitute another reverb pan. It's really important to have the old style, funny shaped 6V6. Of course, that first 12AX7 is extremely important, and the reverb is rarely off."
"....The next button is for the main effect, the Echoplex, which remains on a lot. He'll leave the Echoplex on and hit the loop button on and off to activate other stuff. We use sizzling hot cable — not guitar cable, but hard RF stuff — and we don't lose anything in the loop. From there the signal goes into the Deluxe."
Note that even though the Deluxe is the main amp, the guitar pickup is mostly interacting with the Fender tube reverb unit, as Larry Cragg emphasized by pointing out the importance of the unit's 12AX7 input tube. The Echoplex is also serving dual purpose as a "clean" (tube) gain boost into the Deluxe as well as providing delay. Also note that the reverb (first in fx chain) is placed before the echo (last in fx chain) — weird.