I see no reason for tranny fluid loss to affect the noise of the engine in any way.
did you perhaps drive at 5000rpm for extended periods due to this loss of fluid? did you mistakenly pour the transmission fluid into the gas tank by mistake?
more likely, your fuel filters are dirty, and the car is running rough because of air, or you are paying extreme attention to the car because of the fluid loss, and you are only now noticing the noise.
by any chance are you now driving with the windows down?

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John HAUL AWAY, OR CRUSHED CARS!!! HELP ME keep the cars out of the crusher! A/C Thread
"as I ride with my a/c on... I have fond memories of sweaty oily saturdays and spewing R12 into the air. THANKS for all you do!

My drivers:
1987 190D 2.5Turbo
1987 560SL convertible
1987 190D 2.5-5SPEED!!!

1987 300TD
2005 Dodge Sprinter 2500 158"WB
1994GMC 2500 6.5Turbo truck... I had to put the ladder somewhere!