Today I rolled the JTV59 firmware back to 1.9 and instantly the strat sounds were great.
I now have to use the older edit software which isn't pretty but it works. (The new HD edit only works with the v2.0 firmware).
I didn't notice a huge change in the acoustics.
I've taken screen shots of the strat, ric 12's and acoustic 12's with firmware 1.9 to use in the event that I retry firmware 2.0 with a better result.
Then I can affirm to myself that there are no variables involved other that the firmware itself.
As I can't leave well enough alone, I will probably retry firmware 2.0 later in the week. If the strats work out then I'll be happy, and if not I'll roll back to 1.9 again and be almost as happy.
Also I have (so far at least) got an effective treatment for the problem of the model selector malfunction.
The method of stuffing something into the knob to prevent depressing the knob doesn't address the real problem which is that the frame of the model selector pot is mounted on the underside of the guitar's top using splined hardware pressed up into the wood of the top.
This hardware looks just like a very minature version of the inserts that are pressed into the top face of a Les Paul to allow raising or lowering the bridge.
With repeated depression of the selector knob, these small splined fittngs gradually get pushed out of the wood and into the body cavity.
I reset the fittings in the cavity and then used a liberal amount of epoxy to hold the whole thing in place.
The design seems poorly thought out or insufficiently tested.
I know if I ever have to replace the control, I'm going to have extra trouble getting the epoxy off but for now the repair is flawless.