All SpaceX recipes use module level 1's instead of module level 3's everywhere when you use the mod with Circuit Processing. This is because Circuit Processing iterates over all recipes and replaces "speed-module-3" with "speed-module-2" in its data phase, and SpaceX tries to replace "speed-module-3" with "speed-module-8" in its data-final-fixes phase, but fails to do so because Circuit Processing overwrote the recipe already. It already looks like you have a commented out solution in your code already (hard coded recipes instead of using
bobmods.lib.recipe.replace_ingredient), so maybe you should do that instead.

It does not sound like the fix you are suggesting would work, because if I understand the Circuit Processing mod correctly, there are no "speed-module-8" after it has run its data phase. Instead there are speed modules 0-2 being the equivalent of vanilla, and a new speed module 3. So anything beyond speed module 3 would cause an error. Please advise if I am misunderstanding something here?

The way circuit processing works is that it replaces "speed-module-1" with Speed Module 0 Cable Harness, "speed-module-2" with Speed Module 0, "speed-module-3" with Speed Module 1 Cable Harness, and so on, up to "speed-module-8" being the Speed Module 3.

I get that but it is a timing thing, unless you know that in data-final-fixes phase Circuit Processing will reprocess the speed-module-8s into sm3s, your solution will be left with these undefined speed module 8s.

You define the recipes for the new rocket parts in the data phase, Circuit Processing changes the recipes in the data-updates phase, and you modify the recipes for Bob's mods in the data-final-fixes phase. So I believe everything will make sense if you make the recipe with speed-module-8's hardcoded in the data-final-fixes stage, as Circuit Processing has already made its changes.