I've welded runner floors and roofs also, with both MIG and TIG. I wouldn't try it with MIG again, lots of porosity, hard to control, etc., TIG is way better. The trick is to preheat the aluminum in an oven, I have heated at 300 degrees for an hour or so. Then, when you pull the intake out of the oven, wrap it in a welding blanket so that it maintains the heat. Only expose the port you are working on, and when finished cover it with a blanket, expose the next port, weld, repeat. Keep it covered after welding until it is completely cooled down. Figure on removing 0.040" to 0.060" on the flange to square it up when finished.
I've had to do this with a couple of Dove intakes, where the aluminum was rather questionable, hopefully a Port-O-Sonic would be easier. But its a painful process in any case.
I know you don't want to use epoxy, but in your situation I would. You have to understand that although the epoxy doesn't have perfect adhesion to the aluminum, it does adhere to itself very very well. So, you grind away part of the face of the manifold at the floor, fill that depression with a thick tab of epoxy that will be sandwiched between the intake and the head, then fill the floor of the port. Even if the epoxy wants to try to separate from the aluminum, that tab will hold it in place. Use Splash Zone epoxy, and I don't think you'll ever have a problem with that fill.