Bare EQ Magnum heads vs. machining stock Magnums?

Stock Magnum heads do not have seat inserts, just lightly induction hardened seats from the factory. All stock Magnum heads seam to crack eventually. In most cases, the cracks in stock heads are not a problem, and you can run them a long way like that. The problem is they usually have really worn seats with any real mileage, so you pay to install hardened seat inserts into heads that are good in stock form, but not really worth rebuilding when they are used.
Not sure if the common cracking has caused some of these replacement seats to loosen and fall out, but the EQ heads are better so I personally won't risk it.
As for your stock valves, just have your machine shop take them out and inspect them. The exhaust seats and exhaust valves are usually pretty badly worn. Your machinist can determine if they are still serviceable.