Has the damper ring slipped? Best that I can recall, if it’s an original T-Bird damper then this is likely not the problem. But if there is a ring or something mounted on rubber in which the TDC mark is on and has slipped, then TDC on the damper will not be correct which is automatically throwing off the valve to piston relationship for valve setting purposes. With the #1 cylinder at TDC and at the end of the compression stroke, then the #6 cylinder valves should be equally open. If one of the #6 valves is open more than the other at this point, then top of the list is to recheck the TDC mark on the damper for being correct. If TDC on the damper is verified and correct, then a secondary thing to look for at this point would be the camshaft improperly installed.
Are you confusing the cylinder numbering with the GM’s? The cylinders on the Ford are numbered 1-4 on the passenger side and 5-8 on the drivers side.
Are you rotating the engine by hand? If so, then the engine needs to turn over clockwise looking at the front. If you’re using the starter, then overshooting the 180° and 270° positions by just a little bit will throw off the settings for the valves.
If you’re still having difficulty, then I’d suggest using one of the alternate valve setting methods listed in the following link. I always considered the methodology listed in the shop manual cumbersome as it is ‘Y’ specific and not applicable to the other Ford engines. Some of the other methods listed in the link are more generic in nature and user friendly.
Alternate methods for setting the valves