I do not know positively if this St John cemetery is linked to St John Church - Glendale (7877 Port Wash. rd.). It is an old cemetery next to Tripoli CC on Sherman bvld.
The oldest Lutheran church in Milwaukee (actually several of them) are all located downtown. They were all started in the 1850's & '60s - many of them buried their members at Union (I believe Union was started right after the Civil War). Trinity, St. Peter (now on 76th & Mill rd) and St. Mathew are some of the more well known early Lutheran ones.
Milwaukee county is not my main area of research - I am familiar with some aspects and resources in the county as a number of my ancestors lived there.
Did you just walk Union and Wanderers Rest or did you go through their burial records? I have done both and they are quite extensive.