All,
Fred, this sure is an ambitious project to take on, specially for a first pair. How much of the correction do you expect to get from the orthotic? If you need more correction in the form of high counters and/or ankle reinforcement I would consider an envelope construction. You would take an ankle height last, put the lining and re-enforcements and than just pull an upper without lining over that, western boot style or any other style.
If you go the route of the envelope shoe / boot you can also add to the length of the small foot over the lining to make the boots look more similar in size. Not so much a functional issue but the customer may really like both feet to look the same.
From your description of the foot type I'm wondering if your customer has a rigid midfoot. If so, a slide on boot will be a problem and you may have to resort to a zipper, even it it's going to be a western style boot. (do I hear someone hyper ventilating in the background and where does that teeth grinding sound come from?

) For other foot types a boot with a contoured orthotic should not be a problem to get into as long as you keep a close eye on your measurements when making the last and don't make it to tight. Also make sure your orthotic is firm enough to keep it from getting pushed forward when the foot goes in the boot.
In my experience I would discourage a customer who needs orthotics to get a pull on shoe or boot. Simply because the foot is more prone to move around on the orthotic once inside. For a custom boot this may be different. As my customers generally not qualify or not want a pull on boots my experience with them only goes back to my school days and even that is tainted by my bad memory.
I do not give any extra allowance in my patterns as I make my patterns over the last with the orthotic attached. I make a copy of the last and orthotic, get to a mean forme and base my patterns on that. For a boot I do build up the upper cone of the last and the back over what would be the closing line on a shoe.
One point that Sean brought up and is very useful in a western style boot is the rocker sole. Most custom boots are stiff enough that you get a rocker sole effect anyway but you can always add some to that. The benefit is that you immobilize the foot, once it's in the boot you can probably get away with less aggressive correction compared to a regular shoe / sneaker with an orthotic.
Blake sounds vaguely familiar but the Blake inverted modification does not directly ring a bell, I'll have to look that one up. It's probably one of those thing you know when you hear it but my brain is letting met down. (again)
Arnie Davis does very nice work, I spoke with him on the phone a few times when I was working for a company locally that used him for some custom shoes. It was a no-win situation but considering the circumstances he did very well. I may have seen the PFA book “introduction to pedorthics” once but don't own a copy. Arnie would be a good person to write the biomechanics chapter. When did you work for him, for how long and what did he teach you? He is right that lastmaking can be a bottomless pit but isn't that the same with shoe and bootmaking?
Sean is right on that the terminology is commons sense made to look confusing. If you are slightly mechanical inclined and give yourself some practice you can figure out most things going on in gait. One thing I do before going into heel postion and metatarsal drops is a functional evaluation and determine the type of foot. Looking at the foot as a functional unit, not just at the heel position or the metatarsal position or even the range of motion in the joints, with foot typing you have a very good idea of the foots function and limitations you will find. From there you can go deeper and define the degree of limitation and even deeper go into angles of the heel etc.
Sean, what are the books used in the Canadian Pedorthic education? It strikes me that that Canadian pedorthic system is better organized and provides a more thorough education to turn out a more useful degree when it comes to practical applications and custom shoes. Not that I speak from experience as I have not taken courses on either side of the border but I have worked with Certified Pedorthists from both sides that gives me that impression.
Paul, the cork is very forgiving towards tack holes, pegs may be a different story when you work with Thermo cork. I like to work with the ground up cork in sheet form. It is more forgiving than the thermo cork and offer the customer more shock absorption but will maintain their shape very well, better than EVA's as long as they are secure in the shoe and do not move around.
Fred, I won't be going to the PFOLA, I've used up my travel budget for the year. Not that I would mind going to San Diego but I rather wait till we have a couple of feet of snow on the ground here. That way I get to enjoy the lovely weather and great temperatures even more

. Besides I'm not interested in becoming a volume orthotic lab and the crowd there is certainly not as nice at the Cordwainers were!
Wow, if only I didn't have to do any work I would be able to keep up with the discussion.

I think this was about all I had to say on this topic. (so far) hope it's kind of clear. If not ask!
Rob