Hi Andrew,  It's possible to adjust the notation of a MIDI file with
Cakewalk, using "piano roll" view.  (I've Pro Audio 9 and Windows 98,
but I think it works on other versions.)  It's not a small job!  I did
that on some dance rolls which are short and with a very steady tempo.

First, correct the time signature if necessary (it's easy for a dance
roll: 3/4 for a waltz, etc.  Next, roughly stretch or shrink the
measures to adapt their duration to the notes. (For a dance roll,
"select all" and watch the bass notes.)

I did not find how to do this in one operation in Cakewalk.  You may
use either "fit to time" or "length" in the "edit" menu, but it's
mandatory to correct the tempo in the same ratio to preserve the music.
Then "select all" (mandatory) and "slide" to put correctly the bass in
the first measures.

Last, but not least, do final adjustments on successive selections of
measures.  Don't mind if there are small variations: the score may be
quantized to be "readable" (it's easy with Cakewalk).

For classical rolls with tempo variations, this is a huge work.
A good example of tempo variations is HUNGRAP2.MID in the site
http://www.buczynski.com/~don/proteus.shtml#sequences
(If someone converts this file into a piano roll, I'll buy it, but not
to transcribe rollscan MIDI into music sheet!)

There are probably other methods to do the same job, but I don't
know them.

Good luck !
Jean-Pierre Jouandet