Persoanlly I'd do the supercharger install first for a practical reason:
If your SSR is currently stock, you can then safely install the "normal" tune that Magnuson includes with the kit via a microtuner. If everything does not work perfectly, Magnuson will be able to diagnose the problem(s) because they KNOW the exact configuration you have.
Then, if losing the optional powertrain warranty is not a consideration, go aead and do the exhaust work, BUT understand that you must not drive the vehicle HARD (i.e. high rpm and/or high loading) until you get the air/fuel ratio and perhaps spark timing adjusted by a tuner experienced in tuning supercharged vehicles. This is because IF the xhaust work is done correctly, it will actually increase air flow through the engine, necessitating proportionately more fuel! If that extra fuel is not provided, the engine runs lean, and detonates. THART could lead to massive destruction!
Supercharged engines have a lot less tolerance for lean mixtures than naturally aspirated ones. To give you an idea of how MUCH less tolerant they are, almost all references you will find say that while a naturally aspirated street engine uses about 0.5 lb. of fuel per horsepower hour, a supercharged one should be set uo for 0.6 lb. of fuel per horsepower hour, at least as a starting point until actual dyno testing can be done! That's 20% richer!
This is why Lyndon Wester set up my own 04 modifed and then supercharged SSR so rich as a starting point (Air / fuel ratio of 11.4 at peak rpm at WOT, although more like 11.7 or 11.8 at lower rpm and WOT). He didn't want to blow up my engine!
Going conservative on both air/fuel and aprk advance costs a bit of power - maybe 5 to 7% in my case for example, but is a good idea when:
1. The vehilce is a daily driver
2. The owner is not keen on replacing the engine after it blows up
As I have stated before, there is a REASON that Magnuson voids the powertrain wrranty if the exhaust has been altered at all.
Jim G