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Well you will need a C6 to match your bellhousing bolt pattern, so considering you have an F150 do not get a big-block or a diesel transmission. You will also need to use a PCM from a truck that has the same engine as yours, but a manual transmission, as the PCM you have now operates both the engine and the E4OD transmission and when you put the C6s in it will still "look" for the E4OD and set a bunch of codes and behave god knows how retarded when it don't "find" it. Just a question tho, why replace the E4OD with a 3-speed C6? Kinda makes sense if you have an IDI truck like me and want to entirely do away with electronics, but your '95 has fuel-injected engine that needs a PCM to run it anyways, so you really ain't simplifying things a whole lot with the C6 install... or did the E4OD die on you, and you have access to a good small-block C6?
It isnt going to be a cheap fix to the way the transmission shifts. The cheap "fix" is to find a shift kit to put into the E4OD.
You have to have different drive shafts, then either swap computers or fool your current computer into believing that it still has the E4OD, Chase down appropriate linkages so you can shift the trans into any gear, "new" crossmember to support the trans, etc. As well as expect the truck to be down for any amount of time while you chase parts for awhile.
I'm putting a floor shifter for the tranny and find a manual ecm for the truck. Lifting truck so going to need drive shafts any ways so thats not a big deal. Little work for lot stronger tranny.