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Several questions about the 239, but let's start with questions about using a different transmission. I would like to make the truck a manual, floor shifting truck, instead of using the column shift. Found a Ford 3650, 5-speed manual, but I do not know if those two would mate very well; or easily.
The 3650 transmission is a 5 speed and came out of a 2001 - 2005 Mustang GT or Cobra. Its really not a question if the transmission will mount specifically to a 239 Yblock, but will it mount to any Yblock - an adaptor plate will certainly be needed, and as mentioned a custom drive shaft.
You might have better luck posting this question to the Yblock forum.
What other questions on the 239 do you have? Is it a 1954 EBU 239 or a 1955 EBV 239?
The other thing you have to be aware of if using a Mustang trans is the shifter location. The shifter is pretty far back on the trans, which means it will want to come up under the seat. Not bad if you're running bucket seats and you don't mind reaching beside/behind you, but not so good if you have the bench seat still. That's why the guys who do the T5 conversion opt for the Chevy S10 unit with the forward mount shifter.