Since that shop guy is so far out on his estimate for the repair or the replacement, why take his word that the synchros are bad? You said it was shifting fine. If the synchros were bad, you definitely wouldn't be shifting fine.
If this is just a rationalization to upgrade, then go for the Tremec 3550. It does come with a shifter, just not a pro 5.0 or anything. As far as the transmission mount goes, you can just grind off the welds and reweld it in the correct position.
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351W 89 Mustang GT Convertible