Welcome Craig. Unfortunately you likely have a few issues.
The "standard" MII front end kit is installed such that the lower control arm is basically right at the bottom of the frame. What the vendors call a "standard height" spindle is standard height for a mustang 2, not for the truck. Depending on spring rate/length and adjustment that results in about a 2"-4" drop compared to stock.
The solution that I have seen a few times is to install the MII kit with spacers to offset it below the frame and make up that height difference. If you do a search for user Coilover, he had a post 18 months ago with pictures showing how to do that.
With yours already installed, the initial 2"-4" drop in likely the best you can do without major changes.
Can you post up some pictures of your setup? If so, we might be able to see another solution.
Side note: I would *strongly* caution against just cranking the adjustments to get the height you want by angling the lower control arm down. That does a lot of bad things to your suspension and steering geometry and will give you problems down the road.
