In order to create a standard 11-digit FIPS code for the 1990 data, you will need to add the zeroes to the right of the value. For example, if you have a tract value of “0301”, you would add trailing zeroes to create a string of “030100”.
Are you using Microsoft Excel to manipulate the NHGIS data? The NHGIS data will put quotes around all fields that are supposed to be strings (e.g., state, county, tract). But, Microsoft Excel strips those quotes off the strings when you open the CSV. It then converts the strings to integers, leaving you with values such as “301”.
If you are using Excel, I recommend that you open Excel first and then use the data import tool “From Text” to load the data into the program. This import tool allows you to specify the type of the fields in the file. I recommend setting the TRACTA, COUNTYA, and STATEA columns to Text.
The FIPS codes on the 1990 data are FIPS codes for 1990.