My 94 Honda Civic..which is a 5 speed manual..will crank but not start..It will clutch off and runs and drives well after that. I have to pump the clutch several times before it will even start to crank. I have changed out both of the switches on the clutch housing and even joined the wires together of the lowest switch together. I have changed the battery, fuel pump, fuel relay(the one that mounts near the hood latch), spark plugs, ignition coil, distributor cap and rotor button, and the electronic portion of the ignition switch. Once it jumps off it runs well despite a little surging when it idles( I'll ask for help with the idling problem after I get passed this).
Get the schematics for your car and trace out the starting circuit with a test light. Wondering in the clutch is 'false positive' and the issue is actually somewhere else, or if the clutch is moving a wire.
Your clutch switch will not allow the starter to turn, so if the starter is turning, it is not related to the clutch switch. Your issue sounds to be related to spark or fuel. This sounds like bad grounds to me, but it is hard to be sure without poking around with a test light.