0.040" gasket with 58cc chamber heads and piston 0.050" down the hole = 9.1:1 compression. With a 0.028" gasket would be 9.4:1 compression. Also zero decked 0.28" gasket 68cc heads would be 9.4:1 compression.
There's alot of smaller details here that make this difficult. If you are gonna try and move to a Magnum engine at some part, your probably will not want to put too much into that shortblock. But, you need to get the compression up to increase the power and drivability with that cam. If you mill the 360 heads that much, which is pushin' it imo, your going to have to mill the intake a good amount to fit. Now do you cut and use the iron manifold and make less power or do you buy a Eddy RPM, have to cut that also, and make more power but render it useless on another set of heads because of the milling? As far as carb. i would probably use the 650 on the iron manifold and the Eddy on the square bore manifold. 273 laid out a pretty good plan there and if you went Magnum later you could reuse some of the parts required on the new build. There's lots of opinions on builds like this, maybe some others will chime in also.
P.S. Oh yea, if you use them, the 360 heads you have should easily support the power goal you have set with just a quick clean up and a good valve job.