I have a 2013 Mustang GT with a MT82 transmission I had to pull the transmission due to 2nd gear going out. I rebuilt the transmission and I’m trying to get it back in and I’m running into an issue the transmission is completely mounted up to the engine but when trying to bolt up the cross member the top of the transmission is hitting the transmission tunnel and not allowing the cross member to raise up high enough to get the bolts in. I did just replace the clutch as well I don’t know if that could cause any issues. I added pictures for reference
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