Changing the timing chain at 90-100k miles is intended to fix it before it breaks.
If the engine ran before you replaced the cap I would recheck that job (maybe a missing rotor?)
There are many things that can cause a miss. Plugs (fouled or broken ),plug connectors (burned open), ign. wires (leaking), intake leaks,fuel injectors,fuel distributor and so on.
Good luck Mike