Bubba,
My advice is to start small and work your way up. I have made the mistake of trying to do too much and not succeeding. Keep it simple and you will succeed.
Designing a processor card with PCI, RAM interfaces and the like is no small task. How long it will take you the necessary skills to design a system is up to you but most of all you should enjoy it.
There is plenty of free and low cost software available but you will need to understand electronics first. I second the use of Eagle CAD, it is great for schematics and PCBs.
For simulations, the student edition of PSpice or LTSpice is good for Analogue/High speed. For Programmable logic, Altera, Lattice and Xilinx offer good free software.
I have a near complete design for a scandoubler, admittedly only 16 bit colour though but only uses 4 ICs. Probably a bit complex but if anyone wants the details, I'll upload them to my website.
Ian