C4 Issue No 3rd Gear

I rebuilt the C4 in my 65 mustang about 1 1/2 years ago and it was working great until the new enging was put in it a month ago. it had been parked for 6 or 7 months while I had the students where I work replace the floor pans. Now when I drive it it shifts good still but there does not appear to be a 3rd gear anymore. 1st to 2nd works great shifts around 20 mph on light load and around 55 to 60 at WOT. Low works fine, green dot works fine, reverse works fine, kick down seems to work when in 2nd and punch it, just no 3rd.

I've replaced the modulator valve to rule that out. is it possible there is an issue with the 1 way clutch or possibly a stuck 2nd to 3rd valve from sitting so long? I did have to put fluid in it before driving it. Is there a good way to help narrow down possible culprits of the problem?

thanks,
 
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