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I had this exact phenomenon with my 900ie after a bit of a fiddle with something or other. It was a badly routed cable.
I still think it's cables, not TPS, even though you say you have checked it/them.
Remember that you also have a fast idle cable coming down from the "choke" lever. (It's not a choke, but just increases the idle speed.) Check that it is fully forward and doesn't work it's way open as you ride.
With the engine running move the handlebars from lock to lock and see if you can alter the revs. Any difference will indicate one or both of the cables are tight and need to be re-routed.
With engine stopped open the throttle and let it snap shut to the stop. You can see this visually by watching the quadrant move and listen for the stop hitting. Feel for any resistance or roughness as you open the throttle slowly. Any reluctance to snap back freely or open smoothly could indicate a worn or stiff cable. You can try and lube it but it will probably need to be replaced. Also check the return spring for the quadrant.
I Think I got my cables the wrong side of something or other when I fitted new brake lines. It doesn't take much to upset the free working of the throttle cable in particular, but don't ignore the fast idle either.
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