max_user_connection, when is it a bad script and when is it a busy server.

First I should point out, that 99.99% of the time I have no problems
with my server.
Yes, it is semi busy but nothing that should bring MySQL server down. I
get on average 70 to 100 queries a seconds.

My understanding of max_user_connection is that it is the number of
scripts that simultaneously request a connection, (before the script
ends).
If there is a bug in the script, such as an infinite loop then
connection will be kept until the timeout occurs.

Seen that my server works fine most of the time, I can assume that such
a bug is pretty rare difficult to reproduce. So how can I can it reach
the max number connection?

So my question is, is there a log that keeps track of scripts that took
a long time to run?
I guess anything taking more than 3 seconds should be counted as slow.
A script should never take more than one or two seconds to execute,
(should it?).

And from a database point of view, is there a way of setting a time
out? If the query does not return within 1 or 2 seconds then there is a
problem and it should exit.

And last but not least, Is there a command I my script can send to
flush all the connections regardless of who/what is using it?
Because when that happens then I have to wait a very long time for the
server to recover.

Any thoughts?

FFMG