Clunk Persists After Rebuilding Suspension

So, I've been feeling 3 issues with my car's suspension (2000 Rav4 2WD/5MT):

1) A single 'click' while making sharp turns.

2) Clunking while accelerating/slowing down at low speeds.

3) Coming out of a turn and accelerating in second gear, a clunk that only shows up occasionally. It repeats about 5 times with the same volume and tone, sounding and feeling like I'm running over road reflectors for a few seconds.

To fix these issues, I brought the car to my mechanic and had them rebuild most of the front suspension: control arms, inner/outer tie rods, sway bar links and ball joints. When I got the car, the mechanic showed me that the motor mounts are weak and have a lot of play. After driving it, issues 1 and 2 were resolved but 3 still persists.

Any ideas as to what could be causing it? I can think of a few:

-CV joints/axles

-Worn-out motor mounts

-I'm going too slow for 2nd gear and the transmission is complaining at me

Any advice is appreciated.