The intake/suction sits lower now?
The engine appears low in your pictures, but I don't think it would be a problem. If the former intake setting was indeed higher, it is better now. However, 3/4" is huge and something, either then or now, would be terribly wrong. Is your oil pump hitting any of the front six intake bolts? If your intake is truly set higher, you will run out of clearance in a hurry.
On short drivelines, such as in jet boats, I prefer to keep the angle between 1-3-degrees per joint, not zero. Ideally, for driveline optimization, the pump shaft and crankshaft should be parallel. Here is a really good video explaining U-joint phasing .
I can't tell if you have a 4-point mount or a rail kit from your pictures. The bellhousing looks a little 4-pointish. Assuming that you have a rail kit, you could raise the engine by installing shims between the rails and motor plate blocks. With a 4-point, what you have is what you get.
Something I can't empathize enough: Make sure that you have 1/8" - 3/16" clearance between the slip yoke and bottoming out anywhere on the pump shaft. If it bottoms out, it will destroy your engine!