This worked quite well. Care has to be taken with the SMA loop as it may provide tension and push the post off the center of the hole (the heat shrink tube helps minimize this). The filter loops were slightly tuned and the posts inserted and filter center tuning begun. The following picture shows the final assembly. A top plate was not needed for fine tuning at this point (may be attached in the future with tuning screws to fine tune the response).
The original section tuning was done using an A-B-C stack with the Si application. This is good enough to adjust the inner tubes. As noted by others, use of threads on the tuning rods does cause some problems. The inner tubes do not always make good contact with the base thus creating times when the filter response drops out. This isn't a problem when the jam nuts afix the rods in final tuning. If you apply a slight amount of pressure good contact is made while tuning. My plan was to solder the rods in place (the threads were only intended to hold the rods firmly while upside down to prevent any movement while soldering), however, the nuts have proven to be quite stable so far and provide the ability to modify the tuning in the future so I've elected to stay with them for the time being.
The following is the response as traced by the Si application (previous post on unit #1 includes block diagram). The blue is the response of both sections while the gold (its faint) is a memory of the response with no filter attached. Not shown, is the unattenuated loop where the C-Aux is input to the B RF input directly yields a ~ -50 dB level. This indicates a roughly 8dB insertion loss.
There are a couple of issues going on here. First I could not get both filter sections to fully overlap - I always ended up with the double peak response. This may be due to over coupling between sections (need to go back and do some reading). The other issue is the roll off is not as expected for a two section filter. Part of the concern is the response without the filter (gold line). To investigate this, I used a spectrum analyzer to conduct a manual filter response. Those results compared to the Si results are below.
The baseline response scan (no filter) seems to have a lobed character when you scan out several hundred MHz. It appears there is some kind of bleed through of the C board RF into the B board keeping the base power level high. Before fine tuning this filter or constructing another 2 section filter to cascade I need to spend some time with the Si response.
All in all this approach is better than previous attempts. Using 1/8" brass plate might sound nice and sturdy but it creates a lot of thermal ballast which makes soldering tricky. The material I wish I had read *prior* to starting this is from Sam Wetterlin. He has two documents far down the page that go into great detail on variations on cavity filter construction.