If it's an extended cranking time the solenoid will get hot and kick out the bendix in the middle of the spin resulting in the loud clunk that you hear.
I would get a fuel pressure test, sounds like your pump might be failing. Can you hear the pump cycle before you turn the key to start? It should only run for 1.5 seconds or less if it hasn't lost any of its prime. Longer than that is signs of either a leak on the pressure line, or a failing fuel pump.
'87 YJ, 4.2L built and bored, 8.5" of lift, 8.8 rear, AX15/NP 231, Tom Woods drive shafts, Flat fenders, 12,000LB winch, Custom bumpers, Rattle can paint job. Never completed...