Made Pepperoni Macaroni and cheese again with a different technique, and it came out much nicer
Made a cup of roux, cooked until blond. Added ~4 c
whole milk.  I shredded the cheese (1lb each, cheddar and monterey jack) fine this time and slowly added to the beshamel.
After all the cheese was integrated, I then added the diced pepperoni and simmered.
The sauce was very consistant, and looked fantastic.
The pepperoni still infused the cheese sauce with a nice flavor.
I finished the dish by baking at 350 for 30 minutes.