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I will give you my 2 cents on the lower end upgrades. That stuff is always nice to have and if you can afford it then by all means spring for it! But, IMO the HD chains, backcut tranny, upgraded rods, and stuff like that is really overkill for these bikes. Yea that stuff is cool but man just those chains alone will break your pocket book. My advice is replace the primary chains with OEM, make sure your transmission dogs are in good shape, replace the bearings, primary tensioner, and button it up.
For the head. If you rebuild the the F head you will have no problems. The issues you hear about are due to the valve guide wear. Rebuild with new parts and your golden. If you put on a K head you will need K carbs. The F head spigots are different.