I ran mine with a 5.3 for a long time using dirty dingo adapters, poly mounts and a stock truck oil pan. No issues with pan clearance. It looked low but never came remotely close to any contact. That was with the stock engine crossmember too.
I'm curious what parts you are using too. If it's stirring that low the pan would be riding on the engine crossmember well before the axle would touch it. Collapsed rubber engine mounts can cause it to sit lower. Most aftermarket rubber mounts suck big time these days anyway.
Keep this in mind to getting the engine up higher. You will impact the driveshaft angles on both the front and rear axles. That will require further adjustments to correct.
An LS engine should fit without any issue in the stock SBC location so I'd figure out if the mounts are shot before creating more problems trying to get it higher in the engine bay.