Transcription and pronunciation of the 'un-' prefix in General American English
Solution 1:
Different Americans speak differently. Some have secondary stress on the first syllable of undo, and most other words with the prefix un-, in which case /ʌnˈdu/ is a better transcriptions. See Oxford Dictionary Online. From the comments, some apparently don't. In this case, /ənˈdu/ would be a better transcriptions.
The difference between no stress and secondary stress, and the consequent variation in the quality of the vowel (for those Americans who pronounce /ʌ/ with a different vowel from /ə/) are relatively minor sound changes.