The Core

Mine now keeps cutting out, cleaned fans / heatsinks etc, but this is just not on, lost a lot of work lately, due to processor intensive things going on

The trouble is, i can just upgrade processor, i need to do motherboard aas well.

I was thinking of using the two twin graphicss cards I already have but there is simply a mind boggling selection of hardware out there.

About the only think I know is the form factor.

I dont want to go for 64bit windows in case it is not compatible with anythin I choose to use.

Do you have any tips?

I was thinking

60 ish gb SSD to run win plus office etc
use existing 500gb drives for storage.
Keep graphics cards (but not sure if compatible)
No idea of processor, amd intel etc etc

I have built from the ground up before but I am finding this daunting, there is so much stuff out there

Personally I build a new box with all new stuff. If your existing box has age and stuff is failing, is it worth having another old component start dying in your new rig?

I do leave mine on, running site performance checks and log file dl and analysis and backups and crap like that all night though. So, my main machines run 24/7/365.

I use 64 bit, haven't had any software issues for stuff I run, though I do remember not installing something (don't remember what atm) that wasn't compatible with 64.

Intel procs, personal preference. I've always used them. AMD is better bang for the buck if you're a gamer. Intel is better at multi core performance.

Get as much memory as you want to afford and fits in the mb.

I would go with a ssd for os/apps and a bigger one for data if needed.

Older graphics cards can be iffy if you run them 24/7 and they have their own fans. Again, I like to have all new stuff on a new build and would consider this card:
http://www.newegg.com/Product/Product.aspx?Item=N82E16814139055&cm_re=jaton-_-14-139-055-_-Product

I went for a couple of cheap Acer desktops from Misco this time last year.  I wasn't expecting much, but they are really well built and have been great and up to every job I have given them (I don't play games etc).