Some things to help as I did this awhile ago.
Use short injs. Then you dont need any ex manifold gaskets. They are a BAD idea. They will blow out and you saw how much fun getting that manifold off is. You do NOT need to jack up the motor to do the right side manifold. Take the new ex manifold bolts and cut the studs off the end of them then put them in the manifold first. Use small zip ties to hold them in. These can be removed later.
The crossover issue can easily be solved by a 4 inch lift..
mine has plenty of clearence.
I would STRONGLY recommend ARP studs and new 6.5 HG's. The fire rings are better and the factory printoseal Headgaskets GM used in the 6.2 are garbage. You will blow them. While you already have both ex manifolds off doing the turbo swap it is an ideal time to do the HG's. Imagine having to take all that apart again when your HG's blow, and they will. I run 15 psi boost on mine. he GM turbos are junk and you will find the motor chokes quickly but it is still a major improvement over N/a. I'm gonna play around with an HX35 when funds allow.
Also grab the fuel filter setup off the 6.5. It is far superior to the Box filters these things came with and will eliminate all the problems they cause. Now that you have a 6.5 intake, it will bolt right on. As far as the Battery I used a stock civilian drivers side tray and a smaller batt and kept the one mil batt. The big batts look cool but they are not that great. A civilian batt works fine. I took the coolant bottle from the drivers side and relocated it to the pass side. I had to add one bracket and it looks almost factory.