Perhaps try checking out these two TSB's.
04-16-1 Engine misfire or rough running.
05-15-8 Ticking and/or knocking noise from engine.
Another thing to try is to wait until it is completely dark, then open the hood and start the car (Warning: do not do this in a garage with the door closed) to see if you can spot spark jumping from the coil to ground. I'm thinking the ticking noise you hear could be a spark grounding noise.
Is the ticking noise coming from the top of the motor or from under the car at the front wheel well area?
2005 black GT premium (5spd) / GT500 front LCA/upper strut mounts / Koni Adjustable (yellow)shocks with Roush Springs / FRPP 4:10 rear gear / BMR rear UCA/LCA+relocation brackets / MGW Shifter / Bassani axle backs / Cervinis heat extractor hood and Ducktail spoiler / Carroll Shelby CS69 20x9/20x10 wheels / MSD Blaster 2 coils / Roush TVS2300 Supercharger+Brenspeed 560R upgrade / Exedy Mach 500 Stage 3 Clutch / Exedy lightweight flywheel / SR Performance braided stainless clutch Line / Afco Dual Fan Heat Exchanger upgrade / JLT Catch Can / Axle Exchange one piece aluminum DS / Silly grin on my face every time I turn the key.