I had a very similar situation when I let my bass player connect a separate cab. Ran juice back to the amp. Blew the outer fuse and internal fuse along with a cap. The "smell" made me think it could have blown a cap or 2 also. Mine had a bit of a stink during that sad day. Hopefully your's is just as simple of a fix. The hardest part for me was finding fuses with the exact same rating.
Gotta admit, the redundant fuse inside the chassis was genius on Mesa's behalf.
