1. You should use the ECU, injectors and MAF from the engine you intend to run. Using anything else will give less-than-perfect results.
2. Increasing port size without removing the restrictive component (eg the inlet manifold etc) will do nothing but make the engine 'soggy' and give you no more power.
3. Standard cams are best for a standard engine. Ford did a pretty good job at timing them in from the factory.
4. Machining the head is preferable. You should be able to get away with 1.5mm (on a fresh head) without piston-to-valve contact. You should measure what clearance you do have before making changes.