I have a 2000 Mazda Protege 5 speed with the 1.6L DOHC ZM engine.
I recently changed the timing belt and all associated items (water pump, seals, tensioner pulley, idler pulley) and after starting it up it sounded smooth but upon warming up the RPM's would fluctuate between 700 RPM to 100 RPM and sometimes the engine would stall. This was only after the engine was warmed.
I followed the service manual for lining up the cam shaft and crankshaft marks and with a two wrenches and a vise grip held the cam shafts from moving during timing belt install. The service manual said to line the intake mark at 3'oclock and exhaust mark at 9'oclock so that both marks faced each other. Of course the crankshaft boss mark was at 12'oclock. I even noticed the lobes of the camshafts were facing correctly.
I heard that air bubbles in the coolant system can cause this but after installing a new thermostat (after timing belt change) I'm pretty sure the air bubbles are out.
My order of diagnosis before tearing everything down to get to the timing belt is:
1) check timing with timing light
2) Check for error codes
3) Clean EGR and IAC.
4) Check for vaccum leaks (visual inspection of main inlet hose seemed good)
5) Clean the crankshaft sensor and check gap.
The car ran great before the timing belt change so logically I would think it is off a tooth since I haven't messed with the EGR or IAC and if there were vacuum leaks it would have been there before the timing belt job.
Well I guess I have no EGR valve. I pulled the throttle body off and could not find the EGR valve where it was suppose to be according to the service manual. I'm wondering if someone replaced the engine sometime back?