The factory heads are good heads but by the time you spend the money to prep them for performance, you might want to compare the cost of TFS heads. Their advantages are lighter weight, better heat dissipation and combustion chamber design, hardened valve seats. Bronze guides.
Regardless of which heads you use, checking for proper rocker geometry and push rod length is essential. Camshaft base circle, lifters, head surfacing, block surfacing, milling rocker stud bosses, valve installed height all affect push rod length and rocker geometry. Several articles on rocker geometry are out there and as stated previously in this thread, midlift is one school of thought. Regardless of which method you choose, the most important, in my opinion, is that the wear pattern is not too close to the edge of the valve stem. Also need to ensure the rocker has proper clearance to the valve spring retainer. You also want to make sure the rocker arm slot doesn’t hit the stud through out its travel. With that said, I look for a narrow wear pattern centered on the valve stem to avoid side loading and premature guide wear. I noticed when using aftermarket guide plates, you also want to make sure the rocker lines up with the valve stem. The bottom line is there’s a lot of things to check when assembling your valvetrain to get the best performance while minimizing wear. If you plan on raising your RPM range and using a high lift cam, valvetrain weight is another factor to consider.