I would not mind it sitting a bit higher. I was a surprised about the lack of clearance and maybe that will change when i weld up the engine mounts. I have the front and rear driveshafts installed as a reference front and back. now to try and put in the transfercase mount and see where is sits after that.
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Don't let the driveshafts or crossmember dictate placement. They are cheap and easy to modify. You need to get that engine further back and higher up. Do what Scraps says and get it as high up without making contact with the bellhousing. You're going to have to modify the trans tunnel anyway, so get the motor placed better.