Have 85 Ford with 4 speed manual transmission and a 95 Ford with Automatic. Can I change the transmission from the 85 into the 95?

 

Same engine? That probably doesn't matter too much, as the 4.9 / 300 are the same bolt pattern as the small block. Flywheel would matter, but new ones aren't prohibitively expensive. I'm pretty sure the trans will fit, one big problem with that swap is always the clutch. Hopefully the generation 7 pedal set bolts right up to the generation 9 cab, and isn't the sort that is installed before the dashboard went in. The driveshaft is also of some concern, hopefully some combination of what you have, shaft and yokes will work. Otherwise, it is a lot of poking around scrapyards or having one made. I can't say if the ecm would miss the automatic or not, but I suspect it would be ok

 

Can it be done ? Yes.
Is it a simple swap ? Not even close.
The list of parts you will need to make it work is really long and some of them are really hard to find.
Do yourself a favour and forget you ever even thought about it !

 

I guess the aftermarket could come to the rescue, but as Chris says, this is far from a walk in the park.