Do you have the stock Coyote headers. The swaps I've seen, in magazines and on TV, all seem to use the factory headers and just modify them to fit. I wonder if the stock headers make the computer function better, or easier?

You have three things going against you: headers, 5.0 coyote engine, and Galaxie  with Galaxie being the real issue.  If it was something the aftermarket strongly supports like a Mustang you would be good to go, but being a Galaxie most places don't even list a header for our cars and I am sure not many people have put a Coyote in their Gal to give advice.  I went through this when I dropped a 302 in my 62.  I ended up getting the most compact set of shorties I could find, and even then I had to slightly angle the collector on the passenger side.  I wish some one would chime in with the exact answer you are looking for but I am guessing you are traveling uncharted charted waters.  I would love to see some pix of the install so far.  Even that might help us find something that could be made to work.

If only two primaries need to be modified, then consider yourself extremely lucky. With all the customizing you are doing putting that engine into that car, tweaking headers is a minor thing, and should be expected. Can you get some pre-bent tubing that matches your primary size? Cut and weld to suit.