1998 Lincoln Town Car Irregular Idle

I have a 98 Lincoln Town Car Signature Series 4.6 liter....just recently the engine has started to idle high and low when stopped...it seems to be running to rich...I had it scanned for codes,initialy all 4 oxygen sensors were reported to have failed as well as a transmission code.Since something up stream has caused these codes,a further scan indicated that 4 coil packs were triggered as bad so I replaced all coil packs and spark plugs ( ford parts )....rough idle still exists!!!....I am now being told that the engine computer needs to be replaced ( yikes )...I have also been told that a replacement ECU must be flashed to sync engine and pair of chipped ignition keys.....How far must I go....what about idle control valve....mass flow sensor....does anyone know the flash routine...any advice would be appreciated......thank you.