Which Quicktime bellhousing are you using? There are a few diffrent part numbers that fit Gen3 Hemi to T56.

RM-8074 fits small block to T56 Magnum and is behind my Gen 3. Height = 6.465

RM-6076 small mopar to LS1 T56 height = 5.93"

RM-8077 Gen3 to Viper T56 height = 6.465"

RM-8081 Gen3 to Hydraulic T56 height = 7.339

RM-8078 Gen3 to Mechanical T56
height = 5.525

You may need to get a different bell?