There were Wagoneers offered with the 6cyl and 727. You are right though, you will not have enough clearance. I raised my engine/tranny 1.5" and the front shaft barely clears with the stock springs. I am doing a SOA lift so I won't have any problems. Without any lift the 727 probably won't work.
While you're under there get scrape the gunk off the machined edge of the transmission case below the shifting shaft and above the pan. That's the transmission number... none of the others do any good.
On that flat surface you'll find a number stamped into the side. Copy down the number and take it to D/C to the parts counter. The parts guy can run the number and tell you if it's a 904 or 999. The 904/999 pans are the same, the 727 is different.
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