Yeah, more before the cheese. That might be the problem.

It's the starch in the water, blended thoroughly with the liquid fat, that creates the emulsion. Once the fat/water emulsion exists, the cheese can melt into it. (it's also how ayonnaise is made - except, obviously, egg instead of cheese.)

If the cheese has already begun to clump, it's too late. At that point, if you add heat or starch, the cheese can't slowly melt into the emulsion - chemical reactions in the cheese have already begun to take place.

(Science!)

If you struggle to get it right with pasta water, you could also try mixing in powdered starch before you add the cheese. That will let you experiment with more predictable quantities of starch. It's less traditional, but it's easier to control.