grammar - Punctuating a sentence with a "with" after a conjugation

I'm trying to correctly punctuate the following sentence:

During this time, the rats were also being trained via Pavlovian conditioning to associate a tone and a darkening of the room with the reward being available.

The structure is as follows:

(tone and darkening of the room) with (the reward being available)

As it is, it seems messy as the clauses aren't clearly separated. However, if I were to put a comma after the with it would seem inconsistent since you wouldn't put a comma in a sentence like, "I associated the tone with the reward". Could someone explain the relevant grammatical rules?

Answer

Changing and to as well as and then creating a non-restrictive clause using commas will allow the sentence to be read without the and a darkening of the room part, thus clearing up the confusion.

During this time, the rats were also being trained via Pavlovian
conditioning to associate a tone, as well as a darkening of the room, with the
reward being available.

Relevant grammatical rules
In this case, the only thing needed to be said is that the non-restrictive clause is essentially being paired with the clause before it, so the reader knows the two go together in some way.