The W5A580 is a very performance orientated automatic and doesn't lose very much acceleration in comparison to a manual. If this was going to use a 47RE, then I would say yeah you would lose a lot, but this one isn't too bad from what I have read. As far as the resale value is concerned, I haven't a clue.

How old is this F150 awsure? If it is anything like my Grandfather's 1985 F150 with a 300 cu. in. (4.9L) I6 four-speed manual, then you're dealing with an old, cheap, piece of crap for a manual. You have to fight it to go into first and second. I have driven a few manuals in my day and I can tell you they have improved a lot! I'd say give it a chance and decide when you go test driving.