Exhaust manifold to exhaust pipe bolts too long

I got a TTI exhaust for the car last year and I'm finally getting back to putting it together. Anyhow, on the driver's side the bolts TTI supplied are longer than my old factory bolts and I cannot get one of the two bolts to fit, unless I put it on from the bottom up. I'm thinking this isn't a great idea, so I'd want to know what I 'should' do.

1. Shorten the bolt (cut it? any suggestions on how to do this properly)
2. Replace it with a shorter bolt
3. Put it on upside down......

Exhaust manifold to exhaust pipe bolts too long
Author: jbooth35