FIRST thing i would do is check your manifolds for black soot.
maybe its an exhaust leak??
to check for a cracked flex plate is pretty easy,
with everything you went through i would:
get the engine up to temp so its making the tick you're hearing.
remove inspection plate on the trans,
start it up, and listen
if its still there, take the bolts out of the torque converter,
slide it back as far as it will go and try to wiggle the flywheel.
if it slides back enough, and youre comfortable with it, fire up the engine and listen for the tick.
in my experience with cracked flex plates they make more noise when you put it in gear.
they usually crack around the bolt holes for the crank.
maybe its an exhaust leak??
to check for a cracked flex plate is pretty easy,
with everything you went through i would:
get the engine up to temp so its making the tick you're hearing.
remove inspection plate on the trans,
start it up, and listen
if its still there, take the bolts out of the torque converter,
slide it back as far as it will go and try to wiggle the flywheel.
if it slides back enough, and youre comfortable with it, fire up the engine and listen for the tick.
in my experience with cracked flex plates they make more noise when you put it in gear.
they usually crack around the bolt holes for the crank.