How do I remove the pilot bearing from a 83' 258

Did you change the pilot bearing when you changed the clutch? The pilot bearing is in the center of the flywheel, and the input shaft of the transmission fits into it. If the bearing is frozen, or nearly so, it will cause the input shaft to spin with the flywheel regardless of whether the clutch is released or not. I had this issue on my Dakota, and I had to turn the engine off to get the truck in reverse or first. Once going, the synchronizers allowed me to shift up.
If you can start the engine while in first gear and the clutch depressed and your foot on the brake, then slowly release the clutch and the truck moves, this is probably the issue.
Unfortunately, to replace the pilot bearing, you have to remove the transmission again.

This problem can be viewed at the Honda forum for similar issues with the pilot bearing.

http://honda-tech.com/honda-accord-1990-2002-2/clutch-pilot-bearing-q-2591041/

Gidday, your best bet would be to take it to a mechanic, could be a bearing, the cable, the clutch, some times there is a rubber bush that could get a little sticky at the pedal, try pressing it with the engine off and see if it's still making the sound.

You definitely have a pilot bearing, ask a. Napa dealer to find you one, if they don't see it in the book listed.
its going to be part of the clutch kit you'll be buying to replace your old one.
in the kits you get a pressure plate, release bearing, disc, alignment tool, and pilot bearing, Beck Arnley is a good choice.
if you want just a bearing you'll probably need, the input shaft diameter where the bearing rides, the inner diameter of the flywheel hole it's inserted in, and the depth of the hole in the flywheel.
you should have to much trouble finding one.

You want the clutch, pressure plate and throw-out bearing. I will tell you that on a front wheel drive car it is not the most fun to get everything lined up and the transmission back in there. You need a special tool to line the clutch plate up so the shaft from the transmission will go through it into the pilot bearing in the back of the engine.

You first have to remove the transmission, then remove the pressure plate and clutch disc from the flywheel. the pilot bearing in in the center of the flywheel it can be removed by packing the hole with grease then take a piece of round stock that is slightly smaller than the hole and giving it a quick sharp blow with a hammer this should force the pilot bearing out then wipe out the grease and install the new pilot bearing

Hi David,
I see that you already have several answers to your question. Since you requested an answer directly from me, I'll throw in my 2-cents worth.
I think your dilema is stemming from a case of "partial" bearing/bushing removal and possibly you may have the wrong bearing/bushing in your clutch kit - which is why it does not look right.
Look at the pictures below. The first one is for a pilot bearing ONLY. The second picture is of a pilot bearing/bushing assembly. What I am gathering from your discussion here is that you have gotten the bearing part out and the bushing is still stuck in the end of the crankshaft..
The bushing is made of a very brittle pot-metal and will break pretty easily with a chisel. Just break it into pieces to get it out of the crankshaft. Be careful not to damage the crank. If your kit came with just the bearing like the first picture, then you need to get the bearing/bushing like in the second picture to fix the problem.

The bearing/bushing in the second picture is a MOTORMITE Part Number 14677
It is available at many retail parts outlets including AutoZone.

The pressure plate and release bearing are worn out. You will need a new clutch disc, pressure plate and release bearing. You can either get an estimate from a garage or replace the parts yourself. To replace you will need a transmission jack and mechanics tools.Remove the drive line. Support the engine with a stand and block of wood. Remove the rear bracket. Position the jack under the transmission and loosen the clutch adjustment. Separate the linkages and release bearing fork . Remove the bolts surrounding the bell housing. Carefully back out and lower the transmission. Remove and replace the clutch assembly, and pilot shaft bushing (brass part at the center of the flywheel). You use a wooden dowel or a pilot shaft tool to orient the clutch disc inside the pressure plate while re-installing.

The pilot bearing is pressed into the flywheel and you need a pilot bearing/bushing puller. Some A/P stores will rent it to you for free (deposit). the throwout bearing is held onto the clutch fork normally by clips. Sometimes you have to take the "fork" out to get the bearing off.

Make sure to note how "deep' the pilot bearing/bushing is so that when you install the new one it is set at the right depth.

The squeaking would have either been caused by the clutch release bearing or the pilot bearing in the crankshaft if it has one (pilot bearing). It doesn't really matter as the transmission has to come of to repair either of these. It is hard to tell what you were describing, but whatever you do, don't spray any more WD 40 at anything! It will ruin your clutch and clutch fluid if it comes in contact with either. If the clutch fluid reservoir gets low, only use new brake fluid to top it up.