I have to interject here.
First off: What MAC said. Also, can everyone please stop assuming everyone has the time and skills to do stuff like this. Or even know where to start to get it made locally. Most people don't know what a TIG welder is, or what the difference between sc10 and sc40 pipe is.
Second: My prices on my website assume your starting bone stock. It includes EVERYTHING; cat-back, intercooler, dv upgrade, intake, second cat upgrade, downpipe with cat, turbocharger, tune, uprev license, INSTALLATION, custom turbo adapter, custom intake adapter, Custom cross-over pipe, oil feed/drain lines, custom coolant lines, fluids. Every part you already have brings that cost down significantly, aside from the parts that directly bolt to the turbocharger.
Third: Here is a rotated subaru turbo kit:
link here,~$5000 shipped for what you see and that doesnt cover another $4-5k in parts you will need to take full advantage of it (maxing out the stock engine that is), and the $2-3k to install and tune it. I work very closely with Perry Tuned in Rhode Island. Arguably one of the best Subaru tuners/builders in the country. He laughs every time I show him a thread or email saying my turbo kits are expensive. Go look at a turbo upgrade for a cobalt ss, or a srt-4, or a new gen civic. Not a replacement turbo, AN UPGRADE. A true big turbo. Take that price and call a shop for an estimate to have it installed and tuned. Please, share those numbers when you do. If you want a laugh, go look at the big turbo kits for an RB26. Dumb simpe to make. Hell, I made one for my R32 to save a few bucks. I can tell you it would have been a hell of a lot faster to have just paid for the kit that costs $7000 that only came with the stuff that touched the turbo.
Fourth: Time. Time. Time. I have spent YEARS getting these turbo systems exactly where they are today. Knowing exactly what does and does not work. Trying several different turbo options. Your paying for my time and experience. Sure, a cross-over pipe and intake are a few hundred bucks in material. Okay. What about the $100+ an hour a fab shop is going to charge you to make the pipes fit?
@Macgyver had me install a big turbo system in his car in ONE DAY. In that day I also took 2 hours to fabricate him some custom intake and cross-over pipes. They fit perfect. I can do it so fast BECAUSE I have done it so many times. So again, please call up a local fab shop and get a price on having this stuff made. It takes me a full work day to make an adapter and downpipe. Call it 8 hours. At $100 an hour, that's $800, and that's just the hot side. It would take twice as long to do that ON a car. I have special jigs for every part I need to make. Your paying for THAT. A perfect fitment EVERYTIME. You mention just having flanges cut out. Okay. What about the CAD needed to get it perfect, and the cost of a 5/8-3/4" plate of steel, and the cut time for the flanges. I can tell you right now, if you pay for that process start to finish for ONE flange, your looking north of $200. I know because I had that done years ago before I learned to do CAD myself and purchased the machinery to cut it all myself. Your paying for THAT.
Time. Now lets look at install. By the book its 5.5 hours of labor to do a turbo r and r. That's $500+ (If you need me to I can send you screenshots of two different labor guides with times) If a shop is quoting this install, they are also going to add: intercooler R and R (1.2 hours), Second Cat-Pipe Removal (1.3 hours), and misc. labor for fitting hoses etc., lets call that 3 hours max. 11 hours. So that's lets say a MINIMUM of $1000 in labor, really it will be closer to $1500, most large shops are north of $120 an hour right now. Now find a tuner who would be willing to tune a custom turbo kit like that. Say you find one: $900 is the current going rate for an uprev tune right now, maybe you can find one for $600. So lets ignore all of the fabrication time, and just look at the install, tune, and cost of the turbo parts. $1000 for a BPT 16g, $1000 for the install of JUST the turbo kit with fmic, $600-900 for a tune, $400+ for a FMIC, $1000+ for a second cat-back exhaust. Thats over $3500+ right there. Without fab time. Without the week plus of down time they will have your car to make the stuff, assuming they work that fast.
Now lets include that fabrication time: Your total very quickly is past $5000 on the low end and you still don't have everything you need, nor do you know the cars going to perform because those places have never done this sort of thing before, on a juke specifically.
Time. I have customers bring me their cars and same day they come in with 180 whp, and leave north of 300. Reliably. Your paying for that experience and speed. I have had customers try to DIY a kit. 3 to be exact. Two of them blew their engines up and shipped me the cars to do it right, and one put it back to stock. I know exactly what couplers I need, I know exactly what sc40 reducer i need to go from juke to subaru turbo flanges, I know what clamps I need, I know what hoses i need, I know that I dont need to waste money on aftermarket boost controllers, I know what piping I need, I know the measurements of everything I need, I know how fast I can do it all, and I know the customer wont risk popping an engine because the boost is so damn high. Any of the mamba turbos will need significantly north of 24psi to make "good" power. I can get you to 300 on my dyno for 20. No adjustments, no scaling, the dyno reads it. Want less timing so you dont worry about getting bad fuel? I can get you there for 22 psi on a 16g. And that will be 310+ whp. With torque that doesnt fall off like its a goat following the heard off a cliff.
I had a customer, who I will not name for his privacy, who had another shop build him a 21T turbo set up. He was told he would get 300 whp. Instead he got 285 on their dyno at 28psi, and told his engine had too much blow-by to make an more. A few weeks later, the engine gave out. I FLEW HIM up to my shop to go for a ride in a few big turbo cars. He didn't even make it here from the airport before he made up his mind. No sales pitch. I had a customer pick him up for that exact reason. Genuine experience. He shipped me the car two weeks later. I had his engine rebuilt, tossed on the turbo, made 300+ whp, shipped back the car, and he couldn't believe how much better it performed. He drives it everyday without issue. Total time for the whole process, 3 weeks. Most of that time was waiting on stuff from nissan for his engine.
In conclusion: get a mamba or turbobay turbo, have it tuned, enjoy the bump in power. Hell, I have several used ones here I can sell you for cheap so you can save a few bucks. But when you want to make real power, reliably, take a 3 day trip up here, The car will be a rocket by the time you leave, for a fraction of what your going to pay to have it custom made near you.