I have no experience with a T6060. I have also never installed a LS7 in anything. But geometry requirements remain the same no matter drivetrain is used. Setting aside the engine left to right location. And not knowing if you have lowered the car or not. You can mount the engine is low as you want as long as the crossmember is still protecting the pan. Then its just a case of putting the tailshaft in the right location for optimum driveshaft alignment. If the floor board is stopping that then you really don't have any other options.
Unfortunately, the only way to get that transmission in there is to cut the tunnel to provide clearance, then patch it. There are kits available to do it. I have a T-56 that will be going into my '69 in the near future, and I've already come to grips with the idea that the tunnel is going to require surgery.
I am in the progress of putting a Tremec Magnum-F transmission into my '70 which has similar dimensions to the TR6060. Below is how much I cut (so far) to make space. I will be fabricating a new tunnel from scratch and I'm using a floor brace from Silversport Transmissions that will connect across under the transmission to replace the original floor brace that I cut through (near the shifter area). If you want some dimensions for the cut I can send those do you to give a starting point.