Can't help you with the proper alignment for stock, but if it's even remotely an option to lower them now, I would try that.
No matter what you do, you're likely to end up having to modify something. Whether that something is the fan shroud or the mounts themselves, probably doesn't make much difference. But the mounts might be cleaner (stock looking) than adding a spacer to drop the shroud.
Or, if not a spacer, then at least some type of fastener that lets the shroud fit lower on the radiator itself.
Not sure if the mounts can be fitted lower on the support, as I've never tried it. But the concept is perfectly valid.
Is the truck assembled far enough (engine and body installed) to just test-fit it to your specs?
Reason I ask is that with body lifts, some Broncos act different than others. Just the factory variations at work. Best is to make things to fit YOUR needs while you can.
Good luck!
Paul