So my car was running great started fine every time as well. I decided I wanted to remove the AC and delete the emissions while I replaced my bent shift cables. So I followed the guide on here for removing the emissions stuff, and removed the ac just fine. Buttoned everything back up and wouldn't you know it the battery was dead. So I hooked it up to a known good battery no go. Tried jumping it and no go. It would just click when trying to start it and lose all power. Eventually after the clicking for a very long time it would start to turn kind of.

Here is a video of what it is doing:

 

Certainly seems like a low voltage concern to me. The starter is turning but barely. I would say that second battery you tried is no good, the connections are not good or you left a ground cable off somewhere when doing some of the work.

 

I can't watch the video, Well I could. But I don't have sound on my work computer.

I'd definitely check connections like EatSleepBoost said. Theres an awkward ground in the shifter cable area near the back of the block I saw yesterday while deleting my EGR valve. Check that one out.

 

Tried a new battery, no go. Checked all the grounds etc same thing no start. Now its just clicking when I turn the key.

 

Your starter could be gone or bad connection at the starter. A bad starter will give you a click but that very slow crank in the video sounds like a weak battery. The starter is easy to access so be sure the cables to it are tight. You can try hitting the starter (don't smash it) then try cranking it. Often will free it up for the car to start when you only get a click. If it does start properly replace the starter

 

Take a multi meter and check what voltage you are getting at the starter on the small wire (trigger wire) while cranking.
The video does sound like your battery isn't sending enough amps to turn over the car, but the flip side is that our starters will just click if the voltage is too low. The only time I've ever heard the slow cranking is when the battery was low or when people try and use a small battery that doesn't have enough cold cranking amps. It is possible that your starter is going out, but they normally don't do what your video shows, they just click or do nothing.

 

have you actually measured voltage going to the starter and at the battery? check also for voltage drop by measuring from a known good ground. It may be likely you inadvertenly shorted something when messing around with the emission stuff. check to make sure power is going to the front fusebox, and everything is getting power where it should.

 

I actually pulled the starter and did a bench test and it spun up just fine. I will have to pick up a new multimeter to try, I can't seem to find mine.

 

Can you spin the engine fine using the crank pulley bolt or prying off the flywheel teeth?

 

Yea just tried it moved fine with crank. Spun pretty easily.

 

Then it has to be either the starter, power to the starter or a ground. If it's clicking you are getting signal, now you only have those three things left to turn the engine over.

 

I'll grab a multimeter the starter it's self spins fine when bench testing it. Is there a list of the factory grounds? The ones I could find (Intake manifold, one on the trans, and the main one coming off the battery to the chassis) all seemed fine as well.

 

Sometimes unbolting the grounds and sanding then reconnecting will improve your ground. If you have some wire or a wire with some alligator clips on the end you can clip to the negative terminal of the battery and then clip to a transmission bolt or case to add a ground temporarily for testing. I had one vehicle where this worked, It burnt the test wire quick but proved I had weak ground. I have also seen starters bench test ok but not start the car. I would not rule it out completely yet. If you have a friend with an evo you could ask to try their starter since its quick and easy to change. I would do as follows

-confirm voltage
-try ground test
-try another starter

 

there is a harness behind the intake manifold that might have gotten damaged,disconnected when you were working near that area. Part of that harness has power wires that go from the batt pos. fuse block to the starter,alternator,front fuse box, and acd. There are a few ground wires near there as well, but so long as the battery ground is ok I would think it would at least start up fine. I would also check the fuses on the battery positive terminal, make sure power is going through all of the cables.

 

I agree with your points but for right now all he is trying to do is make the car atleast crank. All testing should be done at the starter then work your way back if you find no power or lack of power to it. Then you atleast know what wire you want to follow. Start at the source you know