This is strange, I had a Hughes deep pan on my 60E before I converted to the 80E.
I had no clearance issues.
Me thinks a second opinion is in order here.
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!