Im about to blow it up!!!
 

So my transmission started acting up again and then it for stuck in gear again and when I was driving It would throw its self out of 3rd gear. It was making a whining noise like a TB so we replaced that. So we get it all back together except for the wheels and we start it up and its still making the noise and it was staying in gear even though it was in neutral so we fixed the gear thing but its still making the noise and I was sitting there with the car running in neutral and it threw itsself back into a gear with no one touching it. Wtf is wrong with my car? I just lost a week of work and I have tomorrow before I have to be back at work and I'm lost. Someone help me before I set it on fire. Could it be as simple as I'm low on tranny fluid? Any ideas? I can't do this anymore. I've never had so many problems with a car.

Check your shift cables... It came un-clipped in my IRL, and I was stuck in 4th gear, no matter what position the lever was in... A TOB can apparently make noise and be fine, Derf has mentioned his rattling when new, and mine makes noise up to about 30mph, unless I go above third gear(it goes away in 4th)...

Are you sure the shifter cable is not binding? If it is getting hung up and flexing (on either the tranny or shifter end), then you THINK you are fully engaged into a gear but you're only 3/4 in and eventually it may spit out of gear. Same story but in "reverse" for the car going from neutral to in gear on its own. Answer?: It was never fully out of gear in the first place, and therefore not really in neutral. It just fell back into whatever gear you last had it in.

Likewise you can get stuck in a gear if the shifter cable is not moving properly and the shift gate is not pivoting properly. Can you move freely through the gears with the car not running, clutch in or clutch out?

Definitely check the tranny fid, but manual trans is basically a bunch of gears bathed in tranny fluid with a circulator forr cooling -- it's not the same level of complexity as an automatic trans with fluid pressure changes and little passages all over the place.

Oh throwout bearing....(thick) used to seeing TOB

We arrived at our answers totally independently and bones owns an ion so go with what he says

No some gears it will go in easily but sometimes I have to make it go into a gear and when I parked it before it took a crap on me it decided it didn't want to come out of first gear like it was locked into place. We were able to finally rock it out. ...I'm at my ****ing wits end honestly. How would you keep the cables from getting hung up?

And as far as the noise....it sounds ****ing horrible. The noise was pretty much going away once I got to a higher gear but it was really bad in 2nd.

How was the shift action while in motion? Go in all gears without too much forcing? My shifter occasionally hangs up when parked, and requires some persuasion to get out of gear/into gear...

I assume you've checked the fluid in the clutch master cylinder... Is the clutch disengaging?

Have you visually inspected your shift cables? They can become un-clipped(I assume it can also be a partial un clipping), and it leaves you with a shifter that does nothing, or doesn't behave like expected(not going completely into gear, etc)

And yeah, my TOB sounds pretty bad in 1st and 2nd gears...

And yeah, not a bad idea to check your trans fluid(not sure what the ION takes, or the capacity, but I doubt our cars are exactly alike due to yours having the Getrag F23 and mine having the Getrag F35)... I should probably check mine too, and possibly change it, as bad fluid can cause a notchy shift action, and gear change issues...

Sounds like the cables. Maybe even the roll pin.
Good luck checking the fluid. Basically need to drop the cradle to do that..unless your Smurf sized.

Idk I'll have him check everything but he said with his research its saying its the input shaft bearing

Interesting read----

DIY: Diagnose manual Tranny Noises (and save some $$$) - Honda Civic Forum

explains which bearing makes noise when and most importantly why.

Mandee, do the sounds come and go as described in this article with respect to clutch pedal position? We already know it has shifting issues
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If it is the Input Shaft Bearing, and I looked it up correctly, NalleyBuickGMC has it for 75 bucks.

Article implies there's a bunch of labor involved--but that's a Honda transmission. But based on the article, the tranny would still have to be pulled and dissected to replace it. So potential low parts high labor cost.