I considered that for my '03 with the six in it, but decided it was too much headache.
My '07 is getting the opposite treatment-- I'm pulling the 2.3 and putting a 3.0 on top. The MTX-75 will happily accept the Duratec 30, as far as I can tell from reading, so everything's happy on the mechanical front, and getting it to mount won't be an issue, either.
Honestly, to do the manual conversion (and to make it look right) will be a huge pain, and will down the car for a bit. Remember, you have details like the PRND on your gauge cluster, the hole for the shifter if it's an '00-'04, linking everything up, et cetera ad nauseum.
I'd try to find one with a stick to begin with. I know it's not the answer you want (believe me, I'm going through an AT/MT conversion in my Camaro, and I hear the same thing about just swap the car out, but I'm too attached to it. You might be in a similar spot with your Escape) but I assure you, it will be the easiest route.
The biggest worry for me is finding a 3.0 of a known good origin. I'm very particular about maintenance, and am a little scared to put just any motor in.
And as far as ECU issues with the trans, I can't say for sure, but I'd think with relative certainty that you'd be correct about it throwing an absolute fit. I've seen ECUs lose their minds over less, and there's a pretty good reason for it to do so. It obviously does not expect you to change the transmission for a different type, and when it can't communicate with the new one, it will think something is wrong with it, and I would think it would go into a self-protective fail-save. I know my mom's old Sebring started stalling itself for no apparent reason when it was having transmission issues. It knew something was wrong, and shut itself down to prevent further damage.
However, this brings an interesting point. Lots of cars use the Duratec 30 and there are manuals among them, so if you acquired an ECU from one of those, I'd think you'd be able to rock the stick.
Whatever you decide to do, good luck. I hope I didn't rain on your parade too much. :thumb: