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Sorry I usually don't try to help diagnose problems with modifieds because there are too many issues that cause probs with swaps. First off the 94 was not obd2. Now you have an obd2 engine/harness installed??? With the stock 94 civic the code 6 would be for the ECT. (Coolant temp sensor) but with your configuration?? Good luck.
Does the engine still run but the water pump is just leaking? The changing it and the timing belt at the same time is only about 2 hours work. But.....if the water pump bearing let go and the timing belt was effected....and you bent the valves...(no more running engine) it is more cost effective to change the whole engine with a low mileage used one.
there are two type of transmission for your 94 civic it's better prefered to use the one with a clutch pump rather than the one with clutch cable their mounting are almost the same and the shift linkage should come in complete set