Help with clicking/tapping noise, 99 2.4 5spd,

Hello Tacoma World,

Got a 99 Tacoma, 2wd, 2.4, 5spd w/ 152K original. I was overseas for 4 years and the truck was placed in a "professional" vehicle storage facility.

Few days after having it back on the road I noticed this tick/click/knock while sitting in a drive through. Few days later, out of the blue, I could not get into 1,3,5 gear. Changed the shifter seat bushing and fixed that instantly. Immediately after I changed that, I did the Trans fluid and put Redline MT-90 or whatever that expensive stuff is thats all over the forums.

Still feels knotchier shifting than I remember and def not as smooth as I'd like, yet somewhat intermittent. But the worst is this terrible click almost tap or knock noise. Sounds like its coming from the front of the transmission housing, around the clutch area. But then again sometimes I feel like maybe its the timing chain?

It does not seem like it goes away with the clutch in or out. It does not seem like it increases with engine rpm. Its a pretty loud fan and motor in and around there and I dont have the best ear for these things but at idle in N or any gear with the clutch in its noticeable. Pretty sure at very low rpm with clutch out its audible as well, rolling around in parking lots and such.

Any ideas how to isolate the click? Or ideas what it might be? Remember it sat for 4 years started and moved 1/month "maybe". Changed the oil, and trans fluid already. Timing chain, valves, clutch or bearing? Thanks!