I don't recall why we positioned the mounts on the frame side the way we did....(don't know if they are considered to be upside down or not). Basically we did what we thought would work at the time.
On the mounts that are welded to the frame, we ended up getting our postion established on one side, relative to (left and right & height) and in order to get the other side to work, we had to fill in one or two of the holes (weld) on the part that bolts to the engine, and then drill a new hole where we filled in...as we could not get the main bolt holes to algin in the stock holes on one side. One side worked...the other would not line up no matter what we did..
We used a tape or string line across the fenders and running forward from the cowl to the radiator support to "eyeball" for hood clearnace. I was very concerned about that and we just barely have enought room to close the hood without interference. I do have decent clearance on the bottom.
If you want some more pics I can take some. My engine is a 99 5.7 Vortec, with GM OEM style air intake. I'm guessing that my engine sits about as high as you can get it, and the GM OEM style air intake allows for tight clearnace at the hood, My air filter mounts on the RH fender well.
I'm running a Mark's adapater too... I think depending on where your engine is lcoated (front to rear) the distance between the frame is different?