My '97 TJ (4-cyl, 5-speed) also clunks in first and sometimes second when accelerating. Only when acceleration is moderate to hard, doesn't do it when accelerating easy or when slipping the clutch. My clunk is from a loose exhaust pipe to exhaust manifold connection; the vibration shakes the whole exhaust pipe and beats the muffler against the transfer case skid plate. Try getting under and shaking/moving the exhaust pipe by the exhaust manifold; if it's loose, then likely there's your 'clunk'.
As walkingstick mentioned, trace the leaking oil to it's source; most often a gasket is to blame and is a relatively easy fix.