This is what I had to have done in order for mine to work:
Not the best pic I know - the pipefitter heated up that runner with a torch and hammered it over a little bit leaving about 1/4" clearance for the alternator. Almost 2 years and 55000 miles later no trouble out of either part
Another issue I had early one (thanks for reminding me bigbird!) was the downpipe portion will run extremely close to the front (closest to the front bumper) engine mount. When I would let off the clutch and coast, the engine and downpipe would touch the front engine mount and cause a loud vibration, but it was a relatively easy fix and didn't have to pay a visit to the exhaust shop again

I jacked up the engine about an inch or so after loosening the mounts and ground the front mount down about a half inch or so with an angle grinder.
I can post pix of this if you want
The MR2 5SFE header will most likely have the same issue since the alternator for an MR2 is mounted differently - it goes close to where the P/S pump would go on our Camrys. You could get the alternator bracket from an MR2 and relocate the alternator yourself, but it seemed like a shitload of work and god forbid it goes out - what a bitch to get to. Plus, if you have any sort of P/S leak around the alternator you can expect to replace that alternator pretty soon