1994 GMC Jimmy ticking noise

My father and husband recently replaced the manifold intake gaskets. While doing that found the the EGR valve needed cleaned and the valve needed replaced. We had to take it to the shop to get this done. After my father had replaced the gaskets a ticking noise which can be heard very well underneath the car started. My father automatically said it was a lifter. He said that while messing with the gaskets and the EGR system that a lifter may have gotten messed up. But the guy at the shop claims it is the flywheel. It is just odd that the ticking noise started until my dad was changing things. I guess my question is does this sound like a flywheel? And if so, how long can it go before messing with the tranmission?