This is my take on a fairly standard CI deck that is about getting bank quickly, getting cards in to your hand quickly, and then setting up a ridiculous server for scoring.
The deck works pretty solidly, and it wins most of the time. The big problem with it is that it's glacially slow. Empires have risen and fallen in the time it has taken me to play some of the games I've used this deck for. But it's silly, and that's why I like it. Just don't expect to take any CI deck to a tournament, I guess.
Ashigaru is key to the megaserver as it gives you a fluctuating but generally large number of subroutines that the runner has to break in order to get in. I think the most I've seen it have is 18 ETR subs, which is tasty in anyone's book. Other than that all ICE is cheapish to rez as you don't want to drop your hand size too much.
Basically unless you are worried about Legwork, Nerve Agent or an Amped Up Wanton Destruction you shouldn't fret too much about ICEing HQ too heavily. There's so few agendas and so many other cards in there that the chances of the runner picking single cards out of HQ consistently is negligible. In the ten or so games I've played with this deck I think I've had one lucky agenda steal happen from a single card HQ pick. Unless they have HQ specific access effects, the runner mostly just leaves it well alone.
R&D is a bit more problematic for obvious reasons coughMediumcough, but Hudson 1.0 is a fairly good counter to that in the short-medium term. He also serves to protect your HQ if Legwork really is going to be a problem. You should only ever need one copy, but wait and see where the multi-access is going to be before deploying. Other than Hudson, Ichi 1.0 and Viktor 1.0/Viktor 2.0 should do for R&D, with Eli 1.0 as backup.
Viktor 2.0 is actually really good early on because a lot of people expect to be face checking an Eli 1.0 at that stage and are often unprepared to meet the trace, especially against your monster econ. Always helpful to have an on call brain damage later on!
Don't ever score Corporate War unless you are sure it will give you the econ boost, otherwise it's a wasted score. If doing so will drop you below 7 credits, try and bluff it out as a failed trap until you can make certain you'll have enough to get the boost. Trust me on this, because if you get down to 6 credits in this deck you're probably in trouble and need the extra dosh.
Traps are there for bluffing out a second Corporate War after you score the first one. Click for credit, install, advance and laugh all the way to the bank as you trash their Desperado. Project Junebug is in there to bluff out as a 5/3 if you have a Viktor token or two in the bank. Install, advance, advance and laugh all the way to the morgue as you do 4 net damage then brain damage them in to oblivion.
The strength of this deck is that it recovers quickly from Account Siphon, as there's so much econ that even if you're reduced to a handful of credits you can just chain operations together to go back to having a monster hand in one turn. I've never had to discard a card from this deck due to hand size limits being reached, even in one game where I got Siphoned 6 (six) times.
It's fun, it'll win you some games, and watching eyes boggle and jaws drop because no-one in your meta plays CI is always good for a giggle.