** UPDATE - FINAL **
So i got home and prayed to the bike gods that I didn't mess anything up. I must be the luckiest mofo alive because the good news is that I did everything correctly...the bad news is that it was just dumb luck...Turns out i had the horizontal pulley exactly where it should have been...That faint mark on the cover was in fact the alignment mark but just got rubbed away after multiple years. I have no idea why all of the tutorials and videos out there reference these stupid marks on the cover when securing the cam is the only sure fire way to do it...
I took off the timing belts and valve covers for both the vertical and horizontal. I checked the valves and they all looked good...within clearance and in perfect shape...I then started scratch from the very beginning. This is the procedure i followed...This was used in conjunction with the workshop manual so it may not be 100% complete...Use it as a guide but not a comprehensive timing belt service...
1) Remove both spark plugs
2) Remove current timing belts
3) Put the bike in the highest gear possible
4) Align the drive shaft mark with the mark on the crank case (This is the only mark you will align)
5) Unscrew the bolt on both the vertical and horizontal cam covers to allow access to secure the cam.
6) You're supposed to use the Ducati service tool to secure the drive shaft so it doesn't move but i didn't have one and it was pretty tight as is and it never moved so i skipped this part.
7) You're also supposed to use the Ducati service tool to secure the cams but i didn't have one and my research of the components led me to believe you don't really need one and a tight fitting drill bit did the job quite well.
With the drive shaft aligned with the mark on the crank case, put the solid part of the drill bit into the access hole to secure the cam on the vertical cylinder. Rotate the pulley on the vertical cylinder until the drill bit engages the hole in the cam. The pulley should lock and you should not be able to rotate it anymore...
9) Repeat step 8 with the horizontal cylinder by using another same size drill bit and engaging the slot on the cam and securing the horizontal pulley in place.
10) With both pulleys secured and the drive shaft aligned with the crank case mark, install and tension the new timing belts
11) Replace the cam access bolts on both cylinders and re-assemble the bike.
The only question i still have remaining is why does the drive shaft need to be secured? It's pretty tight and never moves but the workshop manual calls for inserting the service tool to prevent the driveshaft from moving....It never moves in the first place...Any ideas?