No high pitched whine, never remember having hearing one before.
Car started right up then I turned it off, started it again and did hear a short whine for a split second and it went away, turned it off again started right up, short whine and went quickly away and run smoothly. I haven’t let the car warm up yet

We need to establish the testing method. You should be listening for the whine with the ignition on but without the engine running.

1. Engine not running-cold-inition on. Whine?
2. Engine not running-full warm-ignition on. Whine?

Make a video with good sound quality and post it here. Everything else is reading coffee ground....

No whine on cold start up or after warm up, basically no sound.

If it's running you're getting the whine but you might need to stick your head in the engine bay to hear it well. Open the engine bay, turn the ignition to "on", not "start", (engine should not be running) then get out of the car and listen in the engine bay. The CDI should be whining.

Is the CDI Bosch, Permatune or MSD?

Owned my car over 2 years now and have never heard the whine. Wife says it whines every time. My hearing is shot in that frequency range. So if it quit whining I wouldn’t know it. Just saying, sometimes its not the car thats not working.

Hear! Hear! or should I say No Hear! No Hear!
I'm right there with you.

It's a Permatune

Nevermind. Permatune don't whine.
Do you have access to another CDI that you can swap it out with temporarily?

I replaced the fuel pump just to rule that out, no change still does the same thing.

Check if the frequency valve is working. You could have knocked off the electrical plug on the firewall.

Where is that located

Did you check your vacuum line connections? I had the same symptoms when I removed my WUR, turns out I didn’t reconnect my vacuum line properly. Also, make sure your wiring harness plug connector isn’t loose.

The one's to the distributor?

Refer to https://jimsbasementworkshop.com/CIS/pages/descr_lambda.html

The frequency valve is here named as "timing valve (#11)". This name might confuse a bit. It realizes the the lambda control on managing the mixture for the fuel distributor. It's controlled by the ECU under the passenger seat and is located right behind the air filter box close to the throttle valve. It must be vibrating when engine is cranked and fuel pump is running. If it's not working engine start is hard but not impossible, but the engine won't run on her own without pushing the throttle to keep the engine running.

Get familiar with the lambda CIS as much as you can to get the engine running again. From far away it's pretty hard to find the culprit because in the end - everything on a CIS could be the reason.

I heavily also recommend Curts YT Channel from Klassikats.com:
https://www.youtube.com/playlist?list=PLkWFofpgz2OgF9FdliKnlzuY0pygqRkMj

Although those videos are primarily intended for the 2,7 CIS engines, the priniciples are pretty the same on a 3,0 SC.

Thomas

Might do a quick WUR pressures check. My 83SC was doing the “start but won’t run” thing for a few weeks. Finally figured out the WUR cold pressure was out of spec high and so leaning the mixture too soon. So the car would start on the CSV fuel shot and run for a second or two then shut off. As soon as I lowered the CCP to spec for the ambient temperature it starts instantly and runs perfectly again.

I start the car and let it idle for at least 5 min. and it runs at around 900 rpm without issue. When I give it throttle to rev the rpm's higher the rpm drops to around 600 and the car seems to want to
stall, the rpm seems to go up to 900 and then drop again. If I turn off the car and try to start it again it will not start or stay running without giving it throttle and then shuts off. If I let it sit for 5 min the same thing happens.

I’m with funracer on this one. Maybe you disconnected the WUR or bumped the connection. It is right there where you were working. A pressure test will tell you almost everything you need to know. I had a similar problem and it ended up being the WUR even tho I just replaced the fuel filter. I was 5 psi off and that was the difference between a running car and a stalling car.

Just tried it again an hour ago, started doing the same thing. I went through the same process a few times and then it began running normally. I increased the fuel mixture a bit too increase the RPM's . I decided to take it around my neighborhood to see if it would stall at stop signs and it didn't. I turned it off and waited around 5 min and fired it up again and took it for another drive.
I then left it for an hour and it fired up again and it seems to be running normally again. There is 2 vacuum lines to the distributor, one orange and one black. I noticed when I reconnected the black one yesterday that the end of the hose had a small piece of something that looked like metal. Could that have been the problem?