Usually a pluto user don't recompile it's kernel...so you are probably an exception.
If you want to play with asterisk&stuff, try to checkout trunk/external/asterisk/ from our SVN. There you'll find a "make_package.sh" which will create a deb package for you by recompiling everything for your running kernel.
I'm not sure about other programs you mentioned because it's starting to get complicated.
Let say if there is a vulnerability discovered in apache and we update the package and config files, or we choose to upgrade to php5 or something else happends. such upgrade will probably screw your settings.
You may try to upgrade only 'pluto-*' packages and keep other unchanged... but some of pluto packages REALLY depend on non pluto, pluto-asterisk really expects some configs in asterisk-pluto. IR remote control probably expects latest LIRC and kernel modules (or some specific version of kernel)...there are lots of things that should work together.
So partial upgrade may work for some time...but after a while it will be very dificult to maintain working pluto system and customized server in the same time.
Maybe some virtualization may help??? Like XEN or something. So you basically will run debian as XEN host and pluto as XEN guest.
It's just a suggestion, a have no expertise in this domain, and I DON'T know how to setup XEN, but it looks like most sane solution to your problem (or buy another computer