The issue is that people go through the motions "as they were taught" and never actually learn why each action was taken for the current scenario.
Each process change yields different results so there is no correct answer to the OP's question. "Secondary" can be a vessel or a process, but...
Might as well just use the manual setting on the PID. If you really wanted to you could create a switch circuit to choose what controller you wanted to run the element, but that's a lot of extra parts for no reason. The manual setting on the PID is how I did that for years.
For the boil control I've removed the PID and replaced it with this from Auber...
http://www.auberins.com/index.php?main_page=product_info&cPath=2_30&products_id=444
Makes boil control simple, especially when I have people helping and having them learn the buttons on the PID was...
Using the tri clamp parts, it might be easier to use a tri clamp elbow from the kettle port, and then mount that sightglass on a tri-clamp to NPT thread adapter. Much cleaner and simpler. I will try and make one of those up from parts around the shop if possible and take a pic.
I think to many people get hung up on batch size vs required equipment.
Easy guide for homebrew size is that the vessel volume should be twice the batch size, for any vessel. This means HLT, Mash, Boil.
I see a 10 gallon cooler as the minimum for normal 5 gallon batches and more volume...
You cannot buy too powerful of a burner, but you can't get more heat from a smaller one :-0 Most burners that work well up to 10 gallons are 55k BTU like the basic Bayou Classic, King Kooker, etc. I like the 200k BTU "banjo" models like the KAB from Bayou, or the Blichmann, or the...
Looks solid. A friend suggested this and will be brewing it next week. I didn't see a water profile anywhere (assume Washington DC?), but might not be critical as we have pretty high carbonates here in St Pete and it works well for brewing RIS.