Eventually I hit on an idea. This is hard to explain without pictures, but bear with me....
The upper spring pan and the shock tower are both part of a single bracket. The shock sits inside the spring (as in a standard 105) and pokes up into the shock tower, where it is mounted.
The bracket is attached beneath two of the chassis tubes, bolted to them by 4 bolts, with spacers to set the ride height. The initial assumption was that there was insufficient distance between the spring pan and the shock tower, and the solution was to cut the shock tower and extend it.
What has occurred to me now is that the bracket could have been intended to sit above the chassis tubes rather than below them, but without pictures or access to the car I couldn't clearly visualise whether there was room for it to sit above without fouling anything - there are some diagonal bracing tubes in that part of the chassis and I couldn't recall where they run.
This morning I rang Hugh and outlined the theory. His objection was that the springs would then be too short. This is true, but it was more plausible to me that the springs were cut too short than that the chassis has a major design problem or that the brackets randomly came from another car. Since writing the above I've been in touch with Robert Marsh, the original owner and builder of the car. Rob confirms that both bracket and springs came as-is from the factory, so it looks like this was a design problem. Rob has graciously forgiven me for the implied slur on his mechanical abilities...
Hugh confirmed that the brackets would fit above the chassis tubes, and that this would in fact account for the required 40mm, so this looks like the solution to the problem.
Unfortunately he had already cut the shock towers, and since there are also no correct-length springs handily available, it made sense to keep going rather than change tack now. The car will have stiffer springing than it ideally should (due to the shorter spring), but no more so than before, and extending the shock tower should otherwise be functionally identical to moving the bracket.
For the longer term however, I'd like to put it back the way it was intended. This will mean either modifying the brackets again, or having replacements fabricated. Apart from preferring "originality" where it works, there is a practical advantage to mounting the bracket above the chassis tubes - it makes ride height adjustments much easier, since it won't be necessary to compress the spring in order to add or remove spacers. This is no doubt part of the design, and something I should have thought of earlier. Or not - see note above. This is how the car came, and now it's working I'm inclined to leave well alone. Perhaps if/when I get to the point of changing the rear spring rate I'll look at this again, but until then I'm happy to have a rear suspension that works.