I think the hole saw for the two core lines is probably the best approach. If you have a dremel with the little sanding drums they would be nice to kind of slightly oversize the hole to clean the edges up and smooth them - you may have to get it in from the dash side however.
It may have been overkill but after I installed the heater hoses on my heater I put a heavy strip of 3M strip caulk around them at the aluminum to seal it up tight. It can be a little sticky in trying to mold it to a finished appearance but I found that by wetting my finger with detailer spray or spray wax I could tool it and it also cleaned any smudges off of the aluminum.
It's not necessary but I also fastened a metal strap to one of the upper heater case screws at the rear (dash side) of the heater and ran it up to the inner fiberglass panel in the cowl and secured it with a short screw. That made the heater mounting very solid. With just the 3 screws at the firewall it wasn't as solid as I wanted it to be.
Good luck
Edit - a picture being worth a thousand words - you can see the strap here. I had to be careful where I drilled for the upper mount.
