Q: Knocking noise immediately during acceleration and rolling in neutral. Mounts replaced, no leaks. Ran it on stands only replicate 2001 Mazda Protege

Hello - a knocking noise while rolling in neutral is likely a damaged Constant Velocity joint or a wheel bearing with a "hard spot" or damaged position in the bearing. Acceleration puts additional load on the CV joints, so your "mostly 2nd gear" observation could be a very important clue as well. I recommend a car noise inspection performed by a mobile, professional mechanic, such as one from YourMechanic, who will come to your location, diagnose this problem, and give you an accurate assessment of damage and cost estimate for repairs.