I have done all that you have mentioned...
Roof-
I went with Yakima Load Warrior (the smaller of the two models available), the yakima spare tire adapter, and the yakima lights adapter. Everything has worked well. I have had it all installed for over a year now. I have occasionally taken off the spare tire and put lumber on the roof and it held with bungie cords. I did get some (2) 2x6x12 at one point and the whole basket creaked nonstop on the ride home. Yakima also sells an adapter for the hi-lift jacks.
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On a side note, when I ordered the basket I was sent a basket with a visor that said Subaru. I couldn't return it or exchange it, so I flipped it backwards. After calling Yakima, they sent me some stickers, which worked pretty well. So it says Yakima on the front, but on the back it says Subaru.*
Exhaust-
I did a custom cat back exhaust. I can't remember if the stock pipe was 2 1/4 or 2 1/2, but either way I got a cherry bomb muffler that was dual inlet/ dual outlet 2 1/2. So hypothetically, you could simply use the same/similar muffler for a cheap build. I coupled this with a K&N cold air intake and together they give it a little more power and a better sound.
Painting -
I like towncivillian painted the fender flares and bumpers. I took it a step further and painted the lower half of the door panels. I used premium home depot spray paint. Towncivillian used krylon and someone recently used plasti dip, and so far all have worked. The spray paint I have been using has begun to peel and chip in one spot on my rear bumper so I think it made have just been wet or something when I did it, because everyone thing else is still looking great.
Wheels-
Instead of painting the stock wheels I got new ones. I went with 16" cragar soft 8's.
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