According to Tamiya, the clear and the colors are different formulas, and dry at different rates. It is highly recommended to spray the clear over the last color coat either w/in one hour, or after 2-4 weeks of drying time. Otherwise you run a very real risk of the clearcoat cracking on you, and this is something that may not appear for months, then all of a sudden...
This has happened to one or two people I know, so it is a real concern. I've always applied the clear immediately-as in spray the color coat, take about 5 minutes to put the color away and break out the can of clear, and then mist on a few coats, and then a heavier coat to smooth everything out. I've had the clear attack silver when I applied too much clear at once, you must mist it on a bit slowly. Be patient! But it does work, and since I'm too impatient to wait 2-4 weeks, it's the only way to go. If you accelerate drying, you can be safe waiting a week or so to apply clear. If the clear needs any polishing/recoating, that's not a problem-go ahead and polish out the imperfections, and re-shoot the clear if necessary.
This is not the same condition as the paint bubbling, which happens when the propellant hasn't completely evaporated before it hits the surface...basically meaning you've held the can too close to the surface. The paint levels out nicely, so try holding the can a bit further back.