was it doing this before?

what did the old fluid smell like? Reason I ask many used car sellers that trys to hide a tranny noise like this they add gear oil that smells like rotten eggs and this makes the fluid thicker...

and using the shifter housing is fine, if you look down you will see the gears so your pouring it right on top... In my mustangs,cobras I use 50/50 half an half dextron/Gear oil 80w90 (lucus)Brand and this thickn the fluid for better high temp protection with out tearing the brass in the tranny like full 100% gear oil would do. I would re check the fluid, on the passenger side there is a bottom bolt and a top upper bolt plug. take the top one out with the car level and check with poking your finger in and see if you see fluid on your finger. If not add until it runs out the top hole.

If its full, drain about 1.5 quart out and add that much 80w90.

But these trannys suck assssss T5 T45are the worest ones, and if it still makes the noise you will need new bearings which a used tranny would cost 500ish used