Oh, boy, they want you do it on paper.  Afterwords, I went back to check if I got it all right by plugging into Across Lite.  I actually think it would have been easier to do that way, though you lose a bit of the visual effect.

Anyway, we find the “key” clue at 62-across.  I think I began to be able to say [the answer to 14-Across] (“gotcha” in this case denotes understanding, not some kind of scam or joke) when 39-Across “Preparing to be shot, say” came into focus.

Remember there are many kinds of tubes that might contain warnings.  Some of them, including these, aren’t very close to these shores.

Lots of trick clue/answer combos here.  What I’d call misdirection.  Often your first association to the clue isn’t the meaning the puzzle writer is using.  Some have question marks to alert you to the word play, many don’t.  Ring, Capital of Australia (note the spelling of capital), Shipwreck cause, lightly roast and a couple others fit this description.  So don’t get too hung on a particular meaning of the clue, there may be others.

Private business, in slang:  or “in a phrase”

Knock on wood, say:  Think the sound you make, not the superstition

Face seen on many tee shirts:  If it was 3 letters, you’d know it right away, right?  Same face.

500, e.g.:  As in the ______ 500.

Medical subject of Time magazine:  Note the years, particularly the first one;  2 words

Échecs pieces:  Ok, it’s French.  It’s a game that has pieces.  Each of  these pieces have names you’re familiar with.  The French word here is a very common one.

Melancholy, say:  or joy, you could also say.

Food with an inedible center?:  Very clever.  The puzzler’s right, you can’t eat it, but once you’re done eating, it will be gone!

Very clever, tricky puzzle.  If you had trouble with it, don’t fret, it’s definitely trickier than an average tricky Thursday puzzle.