1. No - but it can be done, with time, $$ and ingenuity.
I'm pretty familiar with the Cougars. You'd be best to get a '67 or 68 headlight assembly to start with. You'll likely have to cut and resize the hideaway headlight components. Also remember the Cougar hood had a bump out in the center that matched the grill center. If you want horizontal ribs, get '69 parts, but that's even wider yet. You'll also have to fab some brackets to hold all the stuff, and either get the headlight switch and all the vacuum components, or - use parts from a ford probe headlight assembly. I know a couple people have gone that route to get rid of the vacuum issue. If a '68 Cougar convertible can be made using mustang parts (it has been done), there's no reason a mustang can't have hideaways using Cougar parts.
Take a look at some of the cars here to get a look at what I mean.
Also, the running cat appeared on the left side of all Cougar grills through '69. You can get two right sides and use one of them on the left to have no running cat.
Expect to spend $300+ for a nice headlight cover assembly
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2. I don't know if early mustangs came with ram air - but again - that can be done if you get a ram air/shaker setup at a swap meet. I'm pretty sure you don't get large increases from ram air - but probably pick up a few hp, in addition to some cooler air in the engine compartment.
3. I'll leave this to those that have more experience in this area.