I loved this game as a young trek fan and am ecstatic that it and others have finally come to gog but after installing it I noticed upon my first play-through that sometimes the audio is a bit choppy or pops slightly, any idea why this might be and what I can do to remedy the situation?

In the DOSBox config file, check if the cycle speed is set to max.

If so, change it to

fixed 10000

That should work fine for a VGA 386 era game.

If the game feels a bit slow, try 15000 or 20000.

I'm not sure why GOG keeps using cycle max, this is known to bug out any game with speed sensitivity issues.