I had those same problems. If you sand fairly deep into the clearcoat, you can just spot paint the places where it's gone through to the primer or where the basecoat seems thin. Then clearcoat the whole part again. I don't know what to tell you about the color deepening--the red I used covers really well--I have some yellow of the same brand and it doesn't.
On my parts that got really awful about boo-boos (hair, dust, bugs) and runs and sags, I ended up sanding the whole panel with a vibrating random orbital sander (electric) and 180 grit paper. I used circular disks even tho the foot of the sander is square--just faster to change self adhesive disks. And then spot painted basecoat as needed and recoated with clearcoat. I'm hoping that the matte surface created by the sander will adhese with the clearcoat.
I figured out why my gun was making such bad orange peel--I was working with too low base (set at the compressor) air pressure, so that the paint wasn't properly atomizing. Will help next time (if that day ever comes again) I need to paint with my HVLP guns.
For the existing orange peel (and there are spots with sandiness from overspraying other parts) I'm using 1500 grit wet or dry with lots of water to keep the paper from loading up. My clearclear coat is a minimum of 6 weeks old, so it's pretty hard. I'm using a two speed polisher with a 12 inch bonnet and I'm using polishing compound to bring up some shine--I'm probably gonna have to use a glazing compound prior to trying to wax. But the process does seem to take the orange peel down to a less noticeable level.
I will be doing some painting this week, gonna paint up a plain hood and a wingless decklid. My spray guns have top vents, too, as they are gravity feed HVLP guns. It really helps to keep the vents clean and properly oriented. My cheap gun from Harbor Freight (about $19) has an aim-able vent and it looks like it's possible to even attach some small diameter hose to the vent. My more expensive gun (a Devilbiss I bought new for about $100) doesn't have the aim-able vent, but it's given no indication of wanting to drip either. If you're having trouble with angles and dripping, prop the hood up a bit to get a better angle--perhaps to 25 degrees (45 degrees is halfway between verticle and horizontal.) Also, only filling the cup halfway will tend to minimize dripping
A short review on my guns--the Devilbiss when properly set up is a really nice gun--but not $80 better than the Harbor Freight one. The Harbor Freight gun works pretty darned well and is certainly okay for the home mechanic. My Devilbiss has a 1 quart metal cup on it--the Harbor freight has a 1 pint plastic cup. I actually prefer the plastic cup, even with paint in it, you can see the paint level in the cup. When painting, I never fill either cup more than 3/4 full--and usually don't fill the quart cup more than 1/2 full. Paint isn't heavy, but 3 or 4 hours of painting makes my forearms cramp up (it's a combination of a motion like hoisting a beer and squeezing a tennis ball for hours at a time.) Loading smaller quantities of paint prolongs the time I can paint (takes longer, tho, too.)
Misc. stuff:
The other thing I found is that those pint and quart cups that cottage cheese and yogurt comes in make pretty nice mixing cups for paint. Base coat has an indefinite pot life--doesn't dry as long as it's sealed up tight, so I store the reduced paint in a clean pickle jar (I prefer Vlasics, btw

) Top coat, of course, gets mixed as I use it (it's catalyzed) can't be stored.
Some shop practices. If possible, put your compressor outside the work area--helps keep the compressor clean, minimizes the exposure of the compressor motor to flammable fumes, and the air is gonna be dryer outside (you are keeping the floor wetted down, right?) Drain the compressor tank every hour or so--more if you live in a damp climate. Use a water trap between your first run of hose (25 feet) and your second run of hose to the gun--the first run of hose allows the air to cool and there will be condensation--and at the water trap, have a pressure regulator to bring the air pressure to a proper level. Then at the gun, there should be another pressure valve and an inline water and oil filter.
And keeping the floor wetted will help a lot, but it's pretty important not to spray the water (no splashing,) just let it flow over the concrete surface--helps keep the dust down and the paint and clearcoat don't want to stick to a wet floor either.