1998 Dodge Neon Neon R/T vibrations under load and full lef

Shakes or Wobbles problem
1998 Dodge Neon 4 cyl Front Wheel Drive Manual 110k miles

My neon recently developed some moderate noise and vibrations in the front when the engine is under a medium load and occasionally on a hard left turn. It vibrates the passenger side floor the most but also the steering wheel, pedals, and shifter. Essentially, it will happen in 4th/5th gear at medium rpms (2000-3000) when the engine is stressed - giving it gas while cruising at 50mph in 5th - the vibrations resolve when the throttle better matches the current rpm for maintaining speed whether straight or up/down hills. It also occurs sometimes when making a hard left at low speed (normal turning like at a light.) It will also never happen when not in gear; the clutch makes it all go away. There is no issue when accelerating in the higher torque/hp rpms either. On a side note my 2nd gear syncro is about destroyed and 3rd is getting bad, but that's been an issue since I got the car a year ago for $700. Wheels, suspension, tie rods, bearings, CV joints, axles, etc. Everything checks out good on a rack. The engine is hard mounted with a performance computer and no rev limiter (found out the fun way tossing belts with the tach needle buried and still revving up; only mention that because it could affect the scanner?) Everything that would normally be suspected for vibrations checks out good (checked and re-checked by myself and a master mechanic.) What's left that I'm missing? Could my nearly scrapped 2nd gear be causing vibrations? There's got to be shredded metal in my tranny but it doesn't add up in my mind. Also, could swapping the motor mounts back to a softer rubber help? Scanner picks up no error codes and the ignition acc on/off produces a 55. What can I try before I replace the whole tranny and axles? I can't get enough rack time to swap it myself and I don't want to pay $500 for the labor.