Just curious on why the fitment issues. I have not got this far yet and while I have only read other posts, there seems to be a lot of discussion that fitment is not an issue overall with certain aftermarket parts. Was something different on yours than those or what makes one work and not another? types of parts, who makes them, or even different conversions from 6 cyl Coyote? Just wondering since I am heading down this path.
Great question... There are a couple of factors that will cause/help with fitment issues which are motor choice and motor mount choice (there's other little things, that's the main ones I ran into). I went with a 2015 F-150 (Gen 2 and was $2,800) which has a different timing cover. The mustang cover puts the alternator up higher and you wont have to notch the frame (unless you use the KE motor mounts). You will however need to relocate the d/s gusset to the front of the cross member if you want to use the factory oil filter adapter. If not, you will need to use an oil filter relocation kit. Both are easily done. The second factor is the motor mount choice. I initially went with Krawlers Edge motor mounts which the motor sits about 2" lower than the Tumblin mounts which I ended up going with. The main reason I decided to go with Tumblin's mounts was I was concerned with the front end pumpkin hitting my oil pan. Tumblins mounts raised my motor up (also increased engine angle to 6.5*) and you wont have to notch the frame for the alternator. That leads to fitment issues with your brake system. With the Tumblin mounts, I was not able to use my vacuum brake booster system as the booster was hitting the d/s engine cover and I wouldn't have been able to pull my dipstick out. I ended up going with a hydroboost which solved that problem. Then if you go with another brand of headers for example, you may or may not have to notch the frame for them.
Like I said, every time I made a change upstream, it always impacted something downstream which had to be addressed. It's not difficult, just a bit frustrating, especially when you order something and think you've figured it out, just to find out you'll need to change it later.
My advice would be to use one vendor and stick with them. Their parts will all jive together. I used parts from Tumblin, KE, BC, Summit, Jegs, etc. I was able to save money going this route, but ran into some fitment issues as stated above. They are all great companies and you won't go wrong with whichever route you end up going. Feel free to PM as well if you have any questions. And good luck, it will be totally worth it!
I will say the first 80% wasnt too bad... The last 20% is taking 80% of the time! 
