First of all, do you have the correct 1953 F-100 bell housing with the motor? You really must start with this. The motor mount setup for 1953 was unique to the F-100 as well as the clutch release parts.
Assuming that you have the 53 bell housing, you could use the flywheel drilled for a 10" long style clutch, but most of the trucks with the 4 speed transmission came with the 11" clutch. If you're planning on using this pickup truck for pleasure driving, the 10" would suffice.
As you've learned, the flywheel that is drilled for the 9-1/2" clutch will not work in the pickup truck. Also, all Ford trucks starting with 1953 models used a longer transmission input shaft (and corresponding deeper bell housing).