One of the rather interesting things I found during the testing for my book was that at least up to 500 HP or so, the medium riser to low riser port mismatch didn't seem to make any significant difference in horsepower. I tried the combination both ways, with a low riser manifold port and a medium riser head port, and also a low riser head port and medium riser manifold port. These mismatches just didn't make a difference.
Probably one reason is that the port flow tends to follow the roof of the port. As the port bends down to aim the a/f charge at the valve, the flow wants to stay along the roof, so what happens along the floor of the port is much less important. You'd think that a mismatch of .300" or so at the floor of the port would really disturb the flow, and maybe it does, but it didn't make a difference in torque or power production.
I would for sure concentrate on a good match between the manifold and head port on the roof and sides of the port, but the floor is much less important. I think I saw your pics on the FE Forum, and I guess the only thing I'd be concerned about is the uneven surface of the floor as a result of the welding. You may have done more harm than good there. I'd either grind the welds out of there and go back to the factory low rise port height, or else get them welded farther in to the port so you can keep the port floor smooth. And definitely widen the manifold ports to match up to the width of the head ports if necessary.
I would be cautious about filling that area with epoxy, by the way. Unless the surface is scrupulously clean and rough enough for the epoxy to grab, you might be asking for trouble there. The intake port can be a violent place, and even in a good epoxy installation any epoxy layer thicker than an eighth inch or so is liable to eventually crack and break off, in my opinion.
I also agree with Bob that the tripower is a definite cork in your combination, but hey, it sure looks cool, and it won't hurt you too badly at the lower speed ranges. Your cam choice might actually be a little strong for that manifold, but I'm sure it will work OK. You will have quite the stump puller there...