Below are answers to your questions in bold.
1) I’m using a Polar M400 to monitor my HR zones. My max HR is 180, and have set the zones up as Recovery <100 (not on the watch as only lets you have 5 zones), Z1 100>135bpm, Z2 136>144bpm, Z3 145>162bpm, Z4 163>171bpm, Z5 172>180bpm. Just did a 1 hour Z1 run and then downloaded it into the Polar Flow website and it listed it as a recovery run rather than an aerobic training session. Is that just a Polar glitch as it’s Zone 1 do you know? Does that sound right for the zone set-up?
First thing is: No need to worry about assigning HR values to Z5. You just go at full max effort, HR is not a good gage for this intensity as these efforts tend to be very short and HR doesn’t have a chance to respond. Emphasis needs to be given to the Z1 and Z2 areas. Percentage of max HR is only a decent guess at these zones but your seem likely. The difference between what qualifies as a recovery workout and a Z1 workout is very much a grey area. Do not worry about this very minor point. Otherwise Zone set up looks reasonable.
2) Calculating training hours. Early this year/late last year I built up over 6 months to 2 strength sessions a week (3 hours max) and 3 runs (6 hours max), so does using 9 hours a week as a starting point sound OK?
Just be consistent. These are your hours and if you always record them he same it doesn’t matter.
3) Do you measure HR during the weight training session? I suspect my HR will not get above 100bpm anyway. And if not I assume you use the time in part of your total training hours calculations?
No, HR is not a good metric of work done in strength training.
4) I have 20 weeks until the trip. I was thinking a 4 week transition > 12 week base > 4 week specific as periods. How does that sound? Should I lengthen transition and/or drop specific? Is 12 weeks base enough? (I’m only doing long easy grade alpine mountains, nothing technical really.)
This sounds like a good periodization plan.