Do you have the stock exhaust?
I ask this because both my stock exhaust and my Dynomaxx LTs both crossed in the space between the crossmember and the transmission pan on the 4L60E.
Since the 80E I installed is longer, the exhaust crossover is about in the center of the pan. I am also running the Hughes deep pan on this transmission and I still don't have any problems with clearance.
I will take some pics and post them if you like, just let me know.
2000 Silverado ECSB, 5.3L, 7" CST/3" PA lift, Hanneman 'glass fenders & bedsides, Currie Dana 60 W/ Detroit Locker, 4.56:1 gears , Willwood Dynalite Pro 4 piston rear brakes, Bowtie Overdrives 4L80E, Nelson Tune & Fan Harness, Harland-Sharp 1.8 Roller Rockers, 2200RPM Converter, Mezerie electric water pump, K&N FIPK II, Dynatech Supermaxx SS LT headers & SS cats, Flowmaster American Thunder cat back, Magnecor wires, Flex-a-lite 282 monster fans, B&M Hi-Tek trans cooler . No DEathCOOL.
And an ls1.com decal on the back window!