You are talking about the front driveshaft contacting the transmission crossmember correct?
Why would lowering (or raising) your shock mounts cause your drive shaft to get any closer or further from the front crossmember? Shocks should not make much of a diffrence in amount of lift you have and if you are using the same old ones it should not change the lift at all.
Are the shocks the proper length for your mounts?
Is it almost touching it when sitting on flat ground? Will lowering it 3/8 be enough to clear when the suspension flexes?
Sounds fishy to me