Tim, you can build one yourself if you think you are capable, I'm not sure how the cost comes out though, I'll have to think out loud from when I built mine. Machine work was about $500 which included balancing the crank, etc, boring .020, cleaning the block and measuring all the clearances for me so I would just have to assemble it and not measure anything. Having them check the clearances was worthwhile, they gave me a sheet with the measurments and the tq values for the mains and rods.
I bought a used cobra crank for $350 which was checked out by the machine shop, rods/pistons (JE/Eagle) were about $900, a cobra oil pump and ford bearings, head gaskets, rear main seal were about $150 I think. I already had head studs (close to $200), got some main studs for free from a friend but you can use stock replacement main bolts if you want to. Not sure what the main studs cost though. Rings were under $100. You have to file fit them, not very hard, you also have to install the spiro-locks on the piston pins. You can reuse most of the other gaskets on the motor such as the valve covers and front cover. So it looks like a little over $2k will build a shortblock if you do it yourself.
Of course now is a good time to get some cams while you have it apart.
96GT with lots of mods