If you are certain the size of your wheel mesh matches the size in the tbc, then I'm a bit baffled as to how the wheels also look high. Some pics would help understand. I have had issues with 3ds Max 9 not correctly exporting something that was scaled. Perhaps somewhere you upscaled the wheels and they are reverting back to the smaller size? 3dsimed was used to confirm the size of my wheels did indeed change, which also confirmed my sanity (in regards to tire sizes)

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Those "ReboundTravel=" distances look pretty big, might I ask the range of ride height?
The graphical offset is moving things 7 cm up (just stating the obvious, sometimes is easiest overlooked).
Those particular undertray points I believe is where rf is measuring ride height. Shouldn't they be Undertray##=
,where ## are numbers.
I would not use corrected inner suspension=-1
http://isiforums.net/f/showthread.php/1078-A-few-questions-looking-for-solutions?p=13267&viewfull=1#post13267-1 seems akin to physically moving the inner suspension pickup points to retain the same suspension geometry whenever you change the ride height. This is something I don't see practically possible. If a chassis builder moves the points they move once for a specific ride height, all other ride heights would then be compromised geometry.
You can rule out the pm file. The geometries of the pm are relocated to the wheel centers.
With such a difference in wheel radius perhaps this is causing an issue? Both ends are floating, correct?
Changing the radii should have a noticeable visual difference. Are you sure the correct file is being edited?