The March sample available in IPUMS-CPS is the ASEC supplement. As you noticed, the number of variables and their names in the NBER March supplement file will not match those in the IPUMS-CPS samples. However, IPUMS-CPS has already taken the extra step of integrating variables over time and across samples by assigning uniform codes to variables. Other than attaching the NBER identifiers necessary to track persons over time, it is unclear why you want to append all of the variables from the NBER March supplement file. Creating an IPUMS-CPS data extract that includes the variables from both the basic monthly survey and the March supplement survey will accomplish what you are describing in a much simpler manner.
Hope this helps. Please let me know if I have misunderstood your question.