Great job so far!
I will try and help where I can but I need some clarity on what's been done so far.
You said you swapped the EGR pipe. Do you mean the coolant crossover pipe? Your 13 should not have an EGR cooler. The 17 does and as such, the plumbing is different. If you are keeping you factory 13 setup you will need to move the coolant crossover pipe from the 13 block and put it on the 17 for the plumbing to be correct.
You said you swapped the alternator to match the new bracket.
The problem I ran into with that, is that the AC compressors are different between the two motors and the alternator bracket from the 17 will bolt to the motor, but will not work with the 13 compressor. Without that bracket you are going to be short one pulley.
On the 13 there is a threaded boss in the face of the timing cover (top center area) for one of the serpentine belt idler pulleys. I had to swap the timing covers from the 13 to the 17 block to maintain the threaded boss for the serpentine belt idler pulley. I posted about this issue somewhere else but not sure where to find that.
Also, depending on the type of failure your original motor had the level of cleaning that timing cover needs will vary. The oil pump is built into the timing cover on the FB20 and Subaru says it's "not serviceable" meaning you have to buy a $500 timing cover if you need an oil pump replacement due to metal contamination. I call BS on that, and have successfully disassembled, cleaned and reused or replaced the "non serviceable" oil pump built into the timing cover. (more on that if you need it)
As for the coils. Yes, the coils and the valve covers are different. The actual spark plug tubes are the same length. I have done both methods you mentioned above.
My preference is actually to cut the harness and splice in the connectors for the 15+ coils. Because it's such a common issue I always do front timing cover and cam carrier reseals on these swaps. I could easily just swap the valve covers at that time and use the original coils.
For me, the reason I don't do that is that I have a personal abundance of the 15+ coils in my spare parts bin. The 15+ coils are much more widely used between many different models and they're actually cheaper to buy new that the 13-14 coils. So for me I just prefer to swap the connectors. That is of course assuming your 15+ motor comes with an intact harness on it.
As for the TGV. As long as you aren't sticking something down there and prying on the valves or taking the mechanical end off you do not have to do any calibration to them. Many times I have seen those codes after a swap and you'll find the connector is not fully clipped. Those TGV connectors have a pretty thick weather pack in there and they need a good press to get them to fully click.
I was helping another person who had the cam sensor codes after this swap. They had swapped over cam sensors, cam phasers and some other things from their motor. I would strongly suggest you do not remove or swap the cam sensors or phasers from your original motor for this swap. The cam reluctor wheels on the 13 vs the 17 are different but they read the same way and are plug n play.
Hope any, some or all of this helps you with your swap. Let me know how it goes!