Bare EQ Magnum heads vs. machining stock Magnums?

Maybe consider what you are putting money into, and if the budget allows a little more for going to new EQ heads.
Used Magnum heads are fine on a tight budget, but I personally would not spend that much for the work you are planning on them. If they were brand new stock castings I would not hesitate.
The factory Magnum valves are not worth spending money on either, although you did not specify if you had stock valves or good replacement valves and springs.
Best value for the long term success, is to contact a shop like IMM or a good local shop and have them quote a pair of EQ heads set up for you with good parts, and see if you can justify the cost.
EQ heads will outperform stock castings when equally prepped.