3900 is a joke ...I am not even going to start. I still think you are taking wrong approach to this. I would start with supporting mods to maximize the stock set up first. THEN once you decide you need more you can get yourself BNR 16/18G and just tune or tune+ injectors and pump in case of 18G. There is simple rule in Subaru world and tunning in general. You either invest minimal amount of cash for stage 2 and good tune, that will net you probably 50hp, 60-80TQ or you are going neck deep and you upgrade a lot of things to get optimal result even from a small turbo upgrade like 16G.
At the end of the day stage 2 setup on stock fueling and turbo will get you similar gains as 16G since new turbo will probably run at 90% efficiency. You might see 10hp more from 16G on stock fueling than on stage 2 setup.
Even if you want to pro tune which is always a good idea, you still want to get AP, since tuner has little bit more sophisticated tool to work with and good tuner might get you little bit better tune on AP than what he would get on open source.
Also, AP will let you switch maps if you go for a road trip and end up in 91 octane only **** hole. 350-400 used and it's money well spend.
Start with AP and downpipe, you won't believe how much stronger and more responsive your car feels. These are 2 things that you will need for any further mods anyway so be smart and start with that.
ANYONE that ever modded subaru will tell you this: "stay stock, stay happy" so stay mostly stock, upgrade DP to let that turbo breath little bit better and fall in love with your car again for minimal investment. After few month it won't be enough so like every other poor soul you will start burning cash for more mods to get 30hp here, 50hp there. Some 2 years and 100hp later, you will realize that you pretty much bought your car again, it's already old and you have to pay for timing belt service, clutch....all that assuming engine, tranny and diffs. hold up. Then you will realize that you could have bought low miles, e46 M3 for all that money you have burned on your econobox subaru with turbo slapped on it. I absolutely adore these cars but you have to be realistic about the mess you want to get yourself in

You are in CO so I feel your pain, stock tune is so miserable in Chicago, I can't even imagine at 5k+ elevation. Trust me, stage 2 tune will put smile on your face.
You're not going to like what I will tell you now but what do you want to do with 300+HP on raised OBXT suspension on CO mountain roads??? You want to have Japanease muscle car that will go fast in straight line and will be pretty pathetic in turns? Stage 2, suspension which will turn your car into LGT wagon pretty much, brakes especially in the mountains and then burn that cash away for further mods
