As someone who is doing this the best way Ive found is to put an Ad on CL. Then when someone wants one you figure out what they will be using it for (Gaming, Editting, General Use, etc) and come up with a Parts list. Then factor in say a 15% increase on the Parts (Parts Price includes All Taxes, OS, and Shipping) and charge them that number. If they dont like the number resell them the value of the PC. Usually after this they pay you (Via Paypal, GW, or Cash. Never Accept Checks) and you begin the process of ordering the parts then building them (Test it as well and Document everything). After its complete Either:
As for Warranty I only give them about a Month and Dont cover anything Software Related. The Warranty is just for Hardware and thats it. It does not cover anything that the buyer does (Like Opening the Case or Tampering with it) and you can mark the Screws so you know (I tend to use Super Glue and stickers). I tend to charge a Premium for a Monthly Warranty service (About $70 a month Base, $100/Month for anything with an OC capable CPU, or $120/Month Premium warranty) instead of going the yearly route.
Now for extra Services:
The Overclocking I tend to charge $40 for just a basic OC (what the motherboard gives you). For a Fine Tuned OC I charge $60 base ($10 increase per part) and goes up by $25/Hr it takes. I make a Killing off of this.
Custom Cables is $40/Cable depending on the Material you want. I do a Hardline Cable type system but Charge a Huge Premium for that since I need to bend Copper, Stainless Steel, or Aluminium tubes as well as Insulate the Cables form the Tubes. This looks incredibly badass too. Have had a few Order this and have always charged $600+ for it.
For Custom Water Price Varies depending on Case and Complexity, If you want soft or Rigid Tubes, ect. Last one I did I made $300 profit.
For Case Modding its the same as Water Cooling. Price varies on Mod.
For a Custom Case it depends on the material, size, features wanted, etc.
In all after all of this said id just recommend not doing it. It makes building them less fun and enjoyable. Its also not steady work and you have to listen to people bitch and complain most of the time. They also blame you for everything when something goes wrong.
Also what most will do is say you cant compete with the likes of the Prebuilts. This is true and you shouldnt even try. Its not about competing with them. Its about differentiating yourself from them and offering value in other areas. Value is not just price.