The only way to protect the GPU vertical mounted if you don't have enough clearance natively to produce decent airflow would be to get a Cablemod Vertical adapter that pushes the GPU backwards, but then you may run into CPU cooler clearance. I would never recommend vertical mounting of an air cooled GPU unless you can provide around 3cm of clearance between it and the side panel if its a solid side panel. If you have this clearance, then you should be OK. I would also flip that top intake and make it an exhaust if you must have it, but having that may actually harm airflow more than help in either configuration due to the turbulence it would create for that top fan. As exhaust, it would just suck a ton of air upwards immediately and cause loss of cooling in the lower half, including the GPU.