HTML5 audio: How to quickly stop and restart a clip?

Wherever you are calling the stop just do the following in the order of -

 n.pause();
 n.currentTime = 0;
 n.play();      

from section 4.8.10.6 of the specification

media . duration Returns the length of the media resource, in seconds, assuming that the start of the media resource is at time zero.

Returns NaN if the duration isn't available.

Returns Infinity for unbounded streams.

media . currentTime [ = value ] Returns the official playback position, in seconds.

Can be set, to seek to the given time.

Will throw an InvalidStateError exception if there is no selected media resource or if there is a current media controller.

So the specification does not allow for seeks of less than one second. However, different browsers will all implement it a different way (of course). Some browsers may support this, but getting it to reliably work in all deployed browsers today will be a huge pain in the ass. Assuming that you could issue millisecond seeks, the other issue is that the js interpreter may not be able to fulfill your request in time, i.e. the processing of the seek takes longer than the value of the seek, which would lead to other difficulties.

My advice to you would be to abandon the html5 approach for now if you really need smaller than one second granularity for your seeks, and use a plugin or some code running natively on the host if at all possible.