I have a 16-17 month old install that I feel may be compromised in some manner and I don't know how to determine if it is or not, so I am assuming that a fresh install should help fix this problem. I also plan on re-installing all other computers on the network at the same time and implementing some more isolated networking structures (I have 5 home networks, 3 ISP and 2 internal)

I have a feeling that there may be some kind of a MITM attack going on and possibly some unknown access to my system when it is locked. I used to log into my web server via SSH and after first login and key exchange, things were fine, then all the sudden I had to accept a new key each time...

So, I don't know if there is a way to do a very high security install with kubuntu (or suggest something more secure or add-on???) or possibly something like adding an IDS/IPS to help determine if something is going on.

If anyone can suggest a method to maximize security I would really appreciate it. I am planning on doing an in-depth "Linux after a year" write up which will include a fresh install and everything I have learned since doing this a year ago - and I think having a more secure install after my first long term use install would be a great addition.

This is for Gentoo, but you may get some ideas.

Well, an obvious place to start is all the articles mentioned at the top in this forum by Unspawn and others.