the pigtail on the coil is commonly an issue...the way the wires are routed they are pulled downward right off the plug connection to the coil and often the insulation on the wires cracks/breaks exposing raw wire.....the current can jump accross these exposed wires causing spark issues. I'd inspect the pigtail and remove the coil....if there are any cracks in the housing of the coil itself then it is bad. A brand new coil from your local auro-parts store should be around $80 if I remember correctly.
if you find issues with either of those and make the necessary repairs and still have issues and want to swap the computer, PM me your computer code and if you have auto or manual trans and I can most likely get you an ECU used for under $100
My majorly huge hand-made Focus RS replica build: http://www.focusfanatics.com/forum/showthread.php?t=289061
My RS conversion is For Sale: http://www.focusfanatics.com/forum/vehicles-sale/578185-sale-rs-mk1-conversion-2003-focus-svt.html