Neat! I'd forgotten just how cute my old BEGI System III+ looked ...
Seriously, its optimum range is in the 8 psi area on a 1.6 liter Miata. Two options:
1) use it as is
2) unbolt the portion of your exhaust between the catalytic converter to the exhaust manifold joint, bolt it to the IHI downpipe you have on the turbo, and have a good shop weld you up a new one-piece downpipe in the size you want.
Personally, I wouldn't waste the time on it; just bolt it up with a cat-back exhaust and drive. The RH5B turbos would max out around 190 rwhp with the rising rate fuel pressure regulator with J&S timing unit and 215 rwhp with the Link computer. This tended to be right on the ragged edge. 160 to 170 rwhp would be found with a system tuned for a large margin of safety with much more peace of mind. Going for more power with higher boost would result in a peaky torque curve as the mass flow fell off at higher rpms.
It's a fast spooling turbo at low rpms and pretty good for autocrossing. It is not a drag racing turbo.
It's your time and your money. For the time and money you put into a custom downpipe you will never get the performance increase you can get by going with a larger turbo. 3" downpipes are sexy and give great bragging rights but an important engineering maxim is..."Better is the enemy of good enough".
I'm not talking down your purchase; it sounds like you got a great deal. I'm on my fourth forced induction system (three from Corky Bell and one (an expensive mistake!) from a competitor) and I'm ready for my fifth (Corky, natch) . I would just hate to see you spend extra time and money for very marginal gains. Every bit of money you saved on the used system will go into "improvements" that don't really obtain you "bang for the buck". Enjoy what you have; Corky did a great job designing that system and you have a classic.
Like I said, it's a great turbo well-mated to the Miata's 1.6 liter engine. I think you'll enjoy it quite a bit no matter what decision you make on the downpipe.
Best of luck to you.