Fox 5.0 1990 T5 manual transmission issue.

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Worn 2nd gear synchro blocker ring
Damaged 1-2 slider teeth
Damaged 2nd gear dog teeth
Broken/damaged 1/2 shift fork.

Only way to know is pull the trans apart and inspect. The longer it goes, the more damage to the 1/2 slider and 2nd gear engagement dog teeth requiring their replacement.
 
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Not good news. I dug into the shifter and found the following pics. The rubber shims being shredded, I am sure due the age and use.
Any chance in your opinion this could cause the issue?
 

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And down the rabbit hole you go...

I can’t tell you how many times I’ve started with replacing one worn item on the foxbody and it led to a chain seemingly endless manual labor...
 
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Do you know if the sell rebuilt kits for this? I have looked online and all I see is replacing the entire assembly.

Many do. Ebay is also a source. Keep in mind you'll need to inspect the gears and sliders and order accordingly as those aren't part of a typical rebuild kit.



 
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Do you know if the sell rebuilt kits for this? I have looked online and all I see is replacing the entire assembly.

Don't go down the money pit too fast. It's one or two parts causing the problem. That shifter needs replacing no doubt. I gave away my last stock shifter 2 years ago on stangnet. You are honestly better off upgrading. Don't get confused with which gear is causing which problem. Most of the grinding issues are "old clutch" related. How old and abused is the clutch in the car? How old is the ctutch cable?

Kurt
 
Do you know if the sell rebuilt kits for this? I have looked online and all I see is replacing the entire assembly.
I think I took that metal and rubber piece off and ran the factory arm on the factory base without it for a bit trying to firm up the shifts. If I remember I put the handle on the driver side of the shifter post. I got some big washers to cover the big holes in the factory shifter arm. You have to stop the slop from the big holes so I found two nuts that were thin enough to sit in the two big holes and were a small enough diameter to be tight in the holes plus cleared the bolts going through.. I put the factory bolts back in I think. That was years ago so I might be wrong on some points. Looks like it'll work from your pics though. Free if you have the bolts and washers. Plus no spongy rubber in the shifter.