When using a plastic bag as a rain cover:

1. Should the external microphone be inside or outside the bag?

2. Is professional grade gaffa tape appropriate to reinforce the plastic around the matt box and in other areas?

3. Are there any other hints and tips you can recommend?

Cheers in advance for your help.

I use plastic bags all the time. Usually I cut a slit in the side of the bag, smaller than the lens hood, and stretch it so the bag will cling to the lens hood. Let that stick out just a little. Tape shouldn't be necessary. I put a bag over the whole camera, and also do a slit for the viewfinder. The way the Canon mic is positioned, you'll probably get noise from the bag hitting the mic, but if you're not moving and the wind's not blowing it will be OK.

Better than a bag, depending on the circumstances, is a golfing umbrella. They're larger than a regular umbrella. You can get an articulated arm and clamp one to your tripod, or use a C-stand, or have somebody hold it.

doesn't sound recorded on a mic inside the bag sound a little muffled?

I guess another slit for the mic should be okay?