I think you need to break this up into multiple questions, because you're about to get barraged by a million different answers, each of them different, lol.
For starters though, you might want to search the forums a little bit. All of these questions have been asked many times. Personally if it were me though, I'd start with the following:
1) Get your motherboard recapped, remove the battery if that hasn't been done already, and get the 64MB hack done. These can all be done by Acill, look for his long thread elsewhere on the forum. The motherboard was originally only designed for 16MB, but can now go up to 64MB thanks to this hack. Any more and you'll need to either add it through an accelerator or a Zorro III expansion.
2) Amiga 4000 PSU to ATX Converter Cable:
http://amigakit.leamancomputing.com/catalog/product_info.php?products_id=615¤cy=USD3) The fans in many A4000's were installed backward - so they blow hot air into the case instead of sucking it out. You'll want to flip that around or replace it with any standard PC fan, off-hand I think it's 80mm. Newegg.com or any PC retailer should have these available, a lot of folks like to replace it with a quieter one, so check the dBA rating on the one you buy.
Have fun!
