First and foremost, if you ever plan on having a Ford service department work on your car after you do the 3L, you had better be very good friends with your service tech.
Most dealerships would have trouble even understanding the what & why behind installing a hybrid engine, and most likely even more trouble understanding a problem that isn't directly out of the Service Manual (which doesn't exist for a 3L hybrid).
Not to say there isn't a Ford dealer out there that is capable of working on it, but you are no more or less likely to have good results with a non-dealership mechanic. And an independant shop will almost definitely charge a lower labor rate than a dealership.
You'd also better understand what you are getting yourself into. Driving a car with any type of non-factory installed engine can and will be an effort in troubleshooting and symptom analysis. What you are doing is getting a variety of systems that were never meant to work together by Ford Motor Company, and make them work together.
Ask anyone who has a 3L, and they can rattle off a significant list of "My car was doing this, it turned out to be this, I fixed it by doing this" stories. Or "I should have done this when I built the motor, so I have to go do it now" stories. Most of them are minor little knick-knack things. Some are major show stoppers. I can think of two people off the top of my head that have had to remove their engine because of problems they've encountered.
I'm not trying to scare you off, but I want to make sure you understand the risk/reward ratio for doing something like this will vary from person to person. I've been lucky: I'm not making as much power as some other people with a 3L but I'm getting great reliability out of the motor, so my project has met most of my goals so far. Daily driver: CHECK. Sub-15 second 1/4 mile: CHECK (heh, barely, I want to improve on that). 200 FWHP: ??? (might be, haven't been to a dyno in over a year).
In my case, my choices were limited, as I was dealing with a blown engine. IMHO, no sense in throwing away a perfectly good engine, especially when there are power making options that can be used with your current engine (S/C, T/C, nitrous). Unless you are looking for a challenge and/or have money to burn.
But keep in mind: Every single 3L is a custom job, so nobody can predict what sort of problems you will run into, if any at all. But really, if a major concern is having a dealership work on it, I'd say just go out and buy a 100hp nitrous kit instead.
