98 Protege hard starting help!
 

I have a 1998 Mazda Protege with a 1.5L. I cannot get the car to start. I have fire at all four plugs and have fuel to the fuel rail. I've removed the valve cover and bumped the #1 piston to TDC. All valves were closed and the distributor button was aiming at the #1 terminal. The cam sprocket Z mark was straight up and the other marks were alligned with the cylinder head. The only trouble code it showed the last time we had it running was for the TPS sensor. We have replaced the sensor, and now the starter will run, but the engine will not turn over. I am completely out of ideas!! Please help!!!

The last time it did run it took forever to get it to start. The engine would just chug like it was trying to start and after about 30 min of starting it would finally catch...

You say the starter runs but the engine does not turn over? That means that the starter cog is not engaging in the fly wheel. Knock on the starter while someone is turning the key. The magnet switch (solenoid) may be bad.

Sounds like a Crank Position Sensor (if it has one).
OR
Did you re-set the ECU after changing the TPS.

Ok here's one to stump your head. I've got the car running... kind of.

You can run the starter while the engine is cold and you can feel the engine "chug" as if it's trying to start. If you push the accelerator to the floor, it "chugs" even more as it's really almost about to turn over. If do this on and off again for around 5 minutes the engine will turn over. And it's always while you have the pedal pressed completely to the floor. I cleared all codes after the TPS sensor was put in, and the only code it shows now is "Random Cylinder Misfire." The engine idles really ruff until it warms up. When the engine is at normal operating temp. it drives fine. You can also turn it off while the engine is warm and it will start right back up. I'm got the timing set to spec, I've removed and cleaned the EGR valve as I thought it was hung open, and cleaned the MAF with some MAF cleaner. But I'm stumped as to what it could be. I've checked the fuel pump and it's working and I'm still getting fire across all cylinders. Any ideas?

I am thinking the ECM is not able to get the air to fuel ratio right when it is cold.

Possible reasons:
Vacuum leak. Check everything between the MAF sensor and the lower intake manifold gasket.
Bad ECT sensor (engine coolant temperature sensor)
EGR stuck open.
Bad fuel injectors.
Bad throttle body.
Bad ignition coils.Yes you have spark but you don't know fro sure if you have enough spark under compression.
Bad ECM.
Bad alternator. A bad alternator could throw the ECM for a loop.
Bad compression.
Bad wiring somewhere.
Leaking fuel pressure regulator.

In the end I would check AGAIN everything going from cheap to expensive to fix. Assume you overlooked something the previous times.