Many, trust me. But not as much as you think.

For one Nav-Point I need 3 Events. One for activation (very simple),
then chained the second which enables autopilot and has between
8 and 12 operators, depends how I would like the ships to act like,
and also chained a third which ends the autopilot and reassign
commands to the ships (around 8 op's).
The problem with this sexp-limit is not really a matter of the
message-number. I have no idea of coding the available
source-code, but I see it like this :
Technically the problem-mission has around 90 messages, and
about 120 events overall (including messages).
First I thougt the counter, which limit I reach is for every single
value that is in the event (4 for each messages in example), but
now that I read the current limit is around 3000, I have not really
an Idea what it counts.
I guess there is much more included like ships, goals, maybe even
the background-data.
Maybe this is a good place to ask for a sexp-controlled
time-compression ? With manuel control the autopoilot is not so
good, because sometimes you missed the correct time to deactive
the time-compression, which can end deadly.

And thank you for the updated version. (btw, has it fixed the
waypoint-display problem already ? )
(edit) on the side-note, must I be worried that the new filesize is
almost only 60 % of the old file ?