In response to Mr. Barrett's request for opinions on Cakewalk programs:
I've been using Cakewalk Professional 8 as a sequencing program for
many years now.  I have not had much success in using it for audio
applications, but I find it's simply wonderful for working with MIDI.
The "piano roll" and staff interfaces are rather easy to use, and the
program supports sound fonts as well.

It sounds to me that you're looking for a program that can quantize
the data from the original roll and line it up with the bars and beats
of the MIDI file.  At the time I write this (Sunday), there's a copy
of Cakewalk Professional 7 at auction with a day and a half left to go.
That may very well be what you're looking for.

I can vouch for the quantization ability of Pro 8 and I must say it
has worked quite well for me.  I think you probably may end up needing
to stretch or shrink the entire roll or sections of it so it lines up
loosely with whatever meter you've chosen (the "fit to time" and
snapping functions come into play here), but from there it's a small
matter of editing individual measures and notes which didn't quite line
up -- glissandos, rolls, and such.

Hope this helps.
Ben Willis
Pennsylvania