While I am far from an expert on this particular topic I do believe that you will find instructions in how to calculate standard deviations (and by extension margin of error) for Census 2000 SF3 statistics in statistical publications from that census that include SF3 data. For example, I have a copy of the Summary of Social, Economic and Housing Characteristics for Massachusetts and Appendix G covers this topic*.
You will need to use tables of both unadjusted standard errors and design factors to estimate the standard deviation included in the Appendix. Once you have calculated a standard deviation and margin of error for a statistic then I think you can use the techniques included in the appropriate ACS publication to compare the values. If your Census 2000 variables are from the long form questionnaire (eg % population over 65) then this method does not apply I believe. In such cases compare the Census 2000 value to the ACS margin of error range.
* You can find similar volumes via Google Books it appears.
I welcome corrections!