Toyota Repair: Toyota 4-Runner Clutch Shudder, toyota fj 40, clutch disc

Question
1993 Toyota 4-Runner 4WD V-6 175,000 miles Cherry Condition.

Had a new engine installed courtesy of Toyota (VO6 head gasket issue) at 112,000 miles.  At the time, the vehicle had a shudder that occurred when letting the clutch out , 1st gear or reverse.  It did not do this all the time.  Had a new clutch disc, pressure plate, T.O. bearing and resurfacing of flywheel done at the time, fully expecting this to resolve the problem (I paid for the parts).  Did not change things at all.  I had asked the mechanic at Toyota how bad my old clutch was worn, he said not much at all.       
Have taken it back many times to dealer but since it does not happen all the time, it will never repeat this symptom while there.  Dealer says if it was in the clutch it would do it all the time.  
Seems to be worse when cold in the AM and also after it has rained.  However some mornings it will not do it (as when I left it overnight at dealer for them to check when cold) and then it will shudder after hot other times.  Symptoms can  
occur at a stoplight and disappear at the next.  
One time a mechanic at this dealer reported that
there was no adjustment left in the freeplay (after I had requested the freeplay be checked) and that the clutch was worn out.  The service manager quickly said that system had air and just needed to be bled which they did.  At times the clutch can feel "weak" as in starting on a hill with passengers in the car.  Weak as in not a strong solid positive feel.  Vehicle currently has 175,000 miles and is in otherwise perfect condition.  I have driven standard trans for my entire life and am not hard on clutches or on the vehicle for that matter.  My  1979 Toyota FJ-40 has the original clutch with 180,000 miles.  I am the 2nd owner of this 4-runner, purchased from a friend at 92K and I know he is not hard on the vehicle.  The shudder ranges from mild to so pronounced that I push the clutch in and try again.What could the problem be?  How should i pursue this?  Did I really get a new clutch with the motor.  Your insight would be appreciated---Axel Johnson  

Answer
The problem may not be with the clutch, it may be an engine misfire or possibly a cracked intake air tube between the air cleaner and the throttle body.
Since the problem was there before the clutch replacement and replacing the clutch didn't help I would assume that the clutch is not the problem and they need to check for the real problem, that's about all the advice I have without actually driving the truck myself.