Do you know, what steps were used confirm the WP is leaking? The WP cannot be seen without first removing the timing cover, and it's likely that was not done. More likely is seeing coolant running from or near the bottom of the timing cover. The problem with that is the thermostat housing is located above the timing belt, and it could be very easy to mis-diagnose this leak, if the coolant is running down from the T-stat housing onto or near the timing cover. This could be the case even if the factory plastic housing was replaced, because it's not at all uncommon for one of the hoses or the housing gasket area to leak sometime after installation. If the leak is from the T-stat, your $800 repair could become $100, or even zero if it's just tightening the bolts or clamps to stop the leak. Regarding the rough running, how long since the spark plugs were last replaced?