I used a Painless kit on my Cobra but on my M6GT I designed my own wiring. While I'll admit that I did some major overkill on the M6GT, the cost of buying all of the proper wire, wire ends, fuse box, and relays exceeded the cost of the Painless kit.
A Cobra is pretty darn simple to wire. No electric locks, no electric windows, no rear defroster, and so on. Do some quick internet searches and you'll find suggested wire gauges for darn near everything in the car. Heck, there is even standard wire colors for a lot of the stuff.
There are ways of keeping the cost down, using one wire color is one way. Using only one gauge of wire is NOT a good way to keep costs down (unless you use 8 awg for everything).
Just don't go out to Radio Shack and figure you'll be able to buy all of the wire you need! Oh, and watch the wire insulation. There are particular types of insulation that work better for cars (where the wire is often subject to temperature extremes as well as vibration and rubbing).
I could probably wire up a car using just 22 awg Radio Shack speaker wire ... but boy would it be ugly as sin!
Go with a Painless (or other) kit.