(1) I suppose that there is a prep process and an amount of baking out time that you would find reasonable in order to get a decontaminated reactor if you didn't have mass spec (just like Deneum did).
How can you tell it is "reasonable"? This is like saying you can see whether the floor is clean or dirty in a pitch black room. When you have no instrument to detect contamination, how can decide whether there is contamination? By ESP?
If you follow the process in (1) and find out that your reactor is still not ready according to (2), then that is evidence that replicators need mass spec.
Or, it is evidence there is some other problem. You have no means of knowing whether the problem is -- or is not -- contamination.
I suppose it would be a bit anecdotal and subjective, but better than nothing.
No, it is worse than nothing. You are saying it is better to flail around in the dark, making mistakes and wasting time with anecdotes and subjective guesses, rather than using the correct instruments.
This is the 21st century. Use modern instruments. There is no reason to be "anecdotal and subjective" when you can use an instrument to see what the situation is.
I cannot understand why anyone would try to do an experiment without the proper equipment. If you cannot afford the equipment, or you don't know how to use it, why would you even try to do the experiment? It seems like a waste of time and effort to me.