I guess I'm headed for a music store to play with a Finalizer. I would
have thought not, but the 'soft limit' indicator was definitely flashing
with some transients.

Since the Finalizer is a tri-band limiter, it will depending on the
threshold settings on the respective bands alter the tonal character of the
transients. Setting them all equal doesn't help either because there are
generally more low frequency transients than high ones in most program
material. Some EQ may help, but you can't really undo the process, course
you know that... As far as the sample rate is concerned, you should be able
to load the files into Sound Forge (I think you use this, right?) and just
set the sample rate instead of resampling if they are at the wrong rate. Of
course if you did any EQ'ing at the wrong rate, it's all mucked up now. If
this is part of your problem, I'm not sure exactly what you meant about the
sample rate issue.