I need to find out where in the boot sequence networking is enabled (ifup)
and where iptables are configured.

Hypothesis:
Runevel S will always be entered at boot time,
followed by one of the other run levels e.g 1 for single user, 2 for standard services.

Therefore networking is started with ./rcS.d/S40networking Right?

[Just curious: what is the reason for ./rc0.d/S35networking (halt)? ]

On my system all iptables policies are set to accept and no other rules exist.
Where is that done? I found no reference in the rc?.d directories.

Thank you

If you investigate a little further you'd see that these 'scripts' in the rc directory structure are really sym-links to /etc/init.d/networking.sh The sequence of the scripts the kernel goes through during boot is indicated by the S followed by a 2-digit number in its name. A script with an S10 prefix is executed before a script with S11 or higher. Same goes for scripts that shutdown the machine, but this time prefixed with K (kill) and again a 2-digit number. Again: the order in which the scripts are executed is determined by the number. General rule in Linux is that the numbers of the S and corresponding K script add up to exactly 100. That is: if you execute a boot script as S75 the K script should be prefixed with K25.

Hint/tip: read the O'Reilly book 'Running Linux'. Recommended!