Mine is about 1/4 Inch above the running surface and I angled the cut ever so slightly upwards toward the rear to account for bow rise while getting on plane.
It works great and reduces the exhaust noise significantly even on the usually pretty tame sounding SN 200. I punched three 3/16” vent holes at about 11,12, and 1 o’clock on top of the hose as close to the existing hull fitting as possible.
I don’t think the vent holes are necessary on your setup as your original pipes are under water anyway, even when the boat is just sitting in the water. It’s a little different with the Nautique, where the original flapper sits just 3/4 under water and when killing the engine air is entering the exhaust. I wanted to keep that situation to not get water sucked up into the exhaust with the silicone elbow.
My advice would be to first cut the “too short” elbows little by little until you are satisfied with the result.
They bend away easily when too long which is not really a problem besides producing a little spray off the stern. (Good visible while skiing behind the boat). If they do, cut some more.
That way you’ll have a “template” where to cut the ones you intend to keep.
*edit*
Pro tip :D for cutting the silicone hose.
Use a new (aka sharp) box cutter. Stuff the elbow with a piece of big pool noodle, put a metal hose clamp around it, position where you want to cut and then cut in one stride along the edge of the clamp. That way you end up with the cleanest possible cut.
(I cut a few times and on 2 different silicone elbows, so I eventually came up with that trick.)