So Oppo, I'm wondering if there's a trans person who could give some insight into this, and if I'm either right, or horribly wrong...

From the beginning:

2004 Dodge Neon SXT 5spd. Bought it from a sort of local dealership, transmission made considerable noise. What did my dad do? Had the dealership check the fluid levels.

Fast forward, car made a ton of noise when cold. Drained the trans fluid, and my dad put in some bastard mixture of motor oils. Made the car quieter. After discussing this with a former trans shop owner, he said it was like putting peanut butter in compared to water. Thicker fluid prevented a portion of the noise.

Fast forward some more...Trans pukes a bearing, three holes in the transmission casing, fluid completely gone, car towed to a trans shop, I had a pulled trans put in. Lasted a good semester until the trans started making noise in the cold. My dad, being my dad, had the trans shop put a brand new trans in the car. Mopar genuine $3300 later, car was back on the road.

Just shy of two years later, hit a deer, car had a shit ton of body work, and the emergency brake cable was stretched out (presumably from the tow truck) but that's not the issue. He claims the trans is making noise again. Trans shop said the car is fine road tested and ready to go. I trust this shop because they treated me very well and come highly recommended.

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I'm suspicious that the output shaft of the motor into the trans may be slightly out, but I could be wildly wrong. I don't beat on the car as I depend on it as a daily driver. There's no reasoning with my dad, so I'm just looking for some clarification from a reliable source about whether I'm crazy or not. I wont be driving it until tomorrow, so I'm not waging any bets on whether it actually is making noise or not, but going by this info, I think someone who knows the ways of the tranny well could wager in on what could be the problem. FWIW, right now, as cold as it is, car makes no noise when starting up. And the wheel bearings are new, so it can't be that...