I lower cars using OEM springs. It does not affect the transmission, shocks, or anything that I can tell.

My first Honda was automatic, and dropped. Made no difference. My present car is manual trans and lowered using OEM springs. Made no difference.

The key to lowering a car is the way a person measures things.
I know how to measure it, calculate the drop, and lower it using stock springs and stock adjusters without destroying shocks, trannys, or anything else.
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Too many people don't know what they are doing, and slam a car below the suspension travel, beat up the shocks and the body, eat the tires, and THAT leads to a bad rap -Bob