Building a PC from scratch is pretty much like following a recipe for cooking a certain dish. Depending on what your needs are for the maximum performance is going to decide on what machine to build and what hardware options you will need to get.
There are two main factors in PC building..Intel vs AMD....Most people tend to steer towards Intel machines due to the stable chipsets that cooperate with the processors. In the world of PC's there is an item on the mainboard which is called a chipset, think of it as the brain. It controls the type of hardware attached to the mainboard, the processor is the heart, it keeps it running. Memory is, well, memory. Like short term memory, the more drugs you do the less short term memory you have, it turns your brain off!! You shut a computer down and no more memory residing in it. Certain chipsets have a way of talking to the PCI bus and if that chipset talks differently than what your audio card needs you will have issues. A lot of people that go with Via or AMD chipsets have encountered certain issues that can not be resolved unless they go with an Intel chipset. Altho today a lot of hardware manufacturers are addressing this issue and writing drivers to fix the problems. I on the other hand dont want to have to constantly add drivers for my mainboard to get it working properly. It makes no sense.
Having been around PC's for quite some time and seeing the problems out there I've attained a serious wealth of knowledge that one can not get just by reading. Just like a Mac, there are certain considerations to take in to count when fixing bugs or crashes(yes, Mac's do crash!!) Building a PC is quite cheap compared to buying a brand new Mac..I saw a G4 733Mhx for close to 3500 smackaroos!! I specked out a Dual PIII 933Mhx system for well under 1,000 smackaroos!! Quite a difference huh?!!
If you know what components you need then go to http://www.pricewatch.com and buy each part that you need, it's probably the best way to go for PC parts.
The key factors are the mainboard, which most people will reccomend Asus or Abit and I will do so as well. Sturdy boards with reliable functionality. Hard drives should be 7200RPM drives and no less!! If you want SCSI remember that you will need a SCSI card which will take up resources on your PCI bus. In todays's specs ATA100 drives are very comprable to SCSI and will do what you need if you are a low track count production. If you do high track amounts then SCSI will be your friend.
Video cards should be AGP, not PCI. PCI video cards can cause issues on your PCI bus by hogging bandwidth. Reccomended AGP memory is no more than 32MB, the higher the video memory the more likely it will cause issues(trust me on this one!!!) I run a 16MB and it runs flawlessly.
Memory should not be a generic brand, Micron is a top seller for memory that I like to go with. CDRoms, well, not much to say really about those, they read. CD Burners, Plextor is the top reccomended brand there.
As far as putting it together, you should read the post Starting from Scratch..it goes over a lot about how you should configure and certain arguments regarding each step.
I dont know what type of knowledge you have now but I think maybe some specific questions will help me help you better.
Going with Logic is an allright choice but be cautious of the learning curve it introduces. Also you can only run Win98SE as of now and soon it will add Win2K support.
Opus

Have you checked out Nuendo? If you want a really serious audio based software I would check it out..it's very very amazing how it handles audio recording and editing. Yes, it is a Steinberg product but it brings Cubase to the next two levels.
Now, as far as what components you should look at: http://www.tascam.com/support/faq/pc_optimize/index.cfm
this was put together by Dave Casey from Tascam and is very indepth about the whole PC process and issues. He has the same ideas and mentality as I do regarding PC setup. Check it out.
Also check out Asus.com for motherboards..click products..then motherboards..then Slot 370. Slot 370 is the new socket processors from Intel and are PIII systems. Most people are opting for the Asus CUSL2 with the Intel 815E chipset. I specked out a system with an Abit BP6 Dual PIII motherboard with two PIII 933's...512MB SDRAM PC133 memory and two 40GB 7200ROM hard drives and came out with around 600 bucks..cant beat that if you ask me. PC prices are very very affordable in every aspect.
Check out Tomshardware.com for bench mark testing and certain products or any thing you need to research.
Opus