One thing to check that was not brought up, since you did or was done a major lowering job, Did you have a custom drive shaft made or are you using a the same drive shaft. I did a my 2003 Dodge crew cab air bags all four corners and 6" body drop. With the lowering and custom 4 link and wishbone suspension, I had to have my 2 piece drive shaft cut down by 1 1/4". You are putting pressure on the main shaft and pushing everything foward into the back of the motor. I have seen trans cracked down the middle on lowered trucks.