I know this is coming late, but I've also just discovered that I over-contributed to my Roth IRA in 2001.

After reading IRA Pub 590, the section titled "Can I Contribute to a Roth IRA?" I noticed this note at the very bottom:

Applying excess contributions.
If contributions to your Roth IRA for a year were more than the limit, you can apply the excess contribution in one year to a later year if the contributions for that later year are less than the maximum allowed for that year.

Can I ask what action you decided on and how it worked out for you? I'm thinking of trying out the solution above.

OLF