A dremel is for hobby stuff. I would not use it on a larger project like this. You will either use up way too many cut off discs (they cost more than full size discs) or you will burn the tool out.
Go with a pneumatic die grinder/cut-off tool, and use the 3" cut off wheels....the thinner the better. Around here you can usually find the tool for sale at around $15 or $20, and the cut off wheels have got more expensive so expect to pay about $1.50 each for those in packs of 5. I remember when I could get those for about $3 a pack, but the chinese seem to now want a living wage.
The cut off wheels will cut in a far more controlled manner than a reciprocating saw. You may have to finish the seams with an angle grinder and a sanding disc. Consider attaching the new panels with epoxy. It is as strong or stronger than a weld, and it has the bonus of sealing the seams.
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