Well, it looks like I wasn't correct about the inlet manifold flanges. The bike's test ride showed improvement but not a fix. I took the bike home and got the throttle bodies out and onto the bench, to go looking for vacuum leaks.
While doing this I noticed that I'd managed to fold and nearly guillotine one of the injector O-rings. These really want grease or similar on reassembly, they roll very easily if they grip on the outside while being installed. However I don't think that this was the problem.
I got diverted briefly by filing off the last remainder of the mould flash lines on the throttle bodies where they connect to the manifolds. Rubber doesn't fold perfectly into the 90 degree valleys either side of a raised ridge like this, even if it's a small feature - a smooth surface is better, even filing by hand. There was dirt at the root of the mould flash line, indicating air movement. These would be pinhole air leaks though.
The greasy dirt around both throttle body return springs finally convinced me to have a look at the shaft seals, as the last remaining place for a significant vacuum leak. The first step was to remove the TPS and get the 8mm push nut off the throttle shaft. There's basically no way to do this without destroying it - I cut both sides of the diameter with a Dremel and broke it away, after failing to lift it by prying with a screwdriver.
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