Grinding noise when trying start.
 

Hey guys I'm hoping someone has someone can help me out. I have a 1993 runner that I just put a rebuilt 3.0 in (I know, I know the 3.0 motors suck). This motor orginally came out of my 90 runner. Before I did the swap I ran the motor in the 90 to make sure she started just fine. She did start just fine and ran for a bit before took the engine out. A year down the road and I fianlly got everything hooked up and the different electronics switched that were different. Last night I tried to start her up for the first time. Before starting I changed the oil and took out the EFI fuse in hope's to turn the engine over and get some oil moving around to avoid any unnecessary damage. The engine turned over just fine and did so about 5 times. I turned her over another 5 times (everything sounded great. I then plugged in the EFI fuse in and turned the engine over some more. The engine did not start. I waited about 30 seconds and tried to start the engine up again. At the last startup attempt there was a loud grinding noise with sorta a high pitch to it. I tried one more time very briefly to start up and see if the same noise occured. The same noise did occur. Any suggestions?? I am thinking maybe the starter could be the issue. I tried to manually turn the crank shaft with the belts off with a breaker bar to see the flex plate teeth and see any damage but to no avail. Maybe having the spark plugs in there is too much compression? I'm hoping I didnt bend a valve or something. Also I did go from a manual transmission to a automatic trans. I switched everything over but maybe I did something wrong? Thanks for reading and if someone can give me some advice I'd really appreciate it.

First, check your battery. You could have run it down, there wasn't quite enough voltage to pull the starter completely engaged, and hence the grinding sound. Use your multimeter; it should be around 12.6v (temperature dependent). If you're below 12.3, I'd put it on a charger.

Bending a valve is not an issue; the 3VZE (an excellent engine, despite your comments) is non-interference. If you had bent the valve outside of the engine, that would just reduce compression.

When you tried to manually turn the crankshaft, were you UNABLE to turn it?

when you swapped it from a manual to an automatic did you remember to remove the pilot bearing?

Grinding noise when trying to start
 

Yes I was unable to turn the engine clockwise like you should be able to do. Maybe the starter gear is stuck out?

Grinding noise when trying to start
 

Akwheeler:

I did not remove the pilot bering.

Oh. That could be a lot of things. You could have left something in the engine, and it could be stuck just about anywhere.

The starter "should" un-stick by rocking the crank, but there's no guarantee there.

At this point, I'd remove the plugs, just to take compression out of the equation. I'd "gently" (gently as one can) try to rock the crank. Is it completely locked? If you can move it at all, does it feel like it's hitting something hard, or just tightening up? Keep an eye on the belts; if they're pretty tight a locked up alternator might be able to keep the starter from turning. You should be able to see them flexing if they won't turn with the crank.

Grinding noise when trying to start
 

I tried to rock the crank back and fourth but I did not get any movement. It will not move at all. The belts are off. My volt meter has I dead battery so I'm going to run to the store now to get that and also get some battery shims. Negative connection was not super tight either. When I get back I will pull the spark plugs and try to turn the crank again.

That may be your issue, I would loosen all of your bell housing bolts to see if you can roll the engine over then.
If so, you need to pull the tranny and remove that pilot bearing.
Most torque converters have a protrusion in the center that fits into the space where the pilot bearing sits in a stick shift application and when you tightened down the torque converter bolts it would bow the flex plate away from the engine block, possibly cracking the flex plate in the process. That would also pull the teeth away from the starter gear causing it to grind and if the flex plate broke it may catch on the back of the block.
When you mate up an engine and automatic transmission the bell housing should meet up with the block without having to pull the two together with the bolts and you should be able to freely spin the torque converter to line up the bolt holes with the flex plate.
With the torque converter pushed all the way into the transmission there is usually about 1/4 inch to 1/2 inch of space between the flex plate and the torque converter but it will pull forward easily to mate up with the flex plate.
If anything is binding or your torque converter is sitting back away from the flex plate and you can't easily pull it forward to touch the flex plate before installing the bolts there is something wrong and you need to figure it out.

did you figure it out yet? did you pull the pilot bearing yet?

I did not pull the pilot bearing yet. I tried to bump start it and after about 2 times of doing that the engine started up. I let it run for a while and started it a few times after that with no issues. I inspected my flexplate and could not find any issues. So maybe a starter issue? Then right before my maiden voyage with the rig she died on me😡 I thought for sure it was the fuel pump so without any further diagnostic I replaced the pump with a Bosch one (the rig looks nice and was garage kept but has 302k miles on her with the original pump) I could not hear the pump turn on so I replaced that and the EFI relay just because. Still no fuel coming out of the fuel line. If I spray starter fluid in the intake she starts. When I put my volt meter to the Male end of the fuel pump line I get noting. Any advice for that? I have power at the relay as well.

You're going to have to go to the wiring diagrams and diagnose it step by step, the VAF is part of the control scheme, start with the fuse first.

What order should that have been in? By the way, your voltmeter CANNOT give you "nothing." It can read 0 volts AC or 12.6 volts DC or all sorts of other things. None of them are "nothing."

Okay, SHOULD you hear the fuel pump turn on? The COR-VAF circuit keeps all voltage from the fuel pump until you turn the key to STArt. (Then you won't hear the fuel pump over the sound of the starter, but hey?) If you just turned the key to ON expecting to hear the fuel pump, you will be disappointed.

First, with jumper wires of some sort, hook your battery to your OLD fuel pump. Does it run? Yeah, you probably replaced a perfectly good pump. (You can do the same with your old EFI relay to get the full experience.) Next, turn the key to on, then jumper FP to B+ in your diagnostic connector. Do you hear the fuel pump now? Try to start it. If it runs, you've diagnosed a problem in the COR-VAF circuit.

(Finally, do a little searching on this site. You'll learn your next step is something like moving the vane in the VAF with your finger with the key ON. If you hear the pump, the problem is in the ignition switch. If not, you'll be using your ohmmeter on the VAF and the COR separately.)