Holy guacamole, your rear springs are 44% heavier than stock, referencing this thread:
http://www.toyota-4runner.org/4th-gen-t4rs/162125-coil-rates-oem-4runner-oem-fj-moog-others.html
The front OME 883 springs are around 1.2" longer than stock, and only a tad heavier. That sounds pretty similar to the height change I did and the truck could still attain factory alignment without a new UCA. Speaking of alignment:
Agreed... looking over the image of his alignment specs, it does seem pretty close to spec (assuming the specs on the left column are true).
I'm really thinking your rear springs are too stiff. Do you have a full-size k02 275/65/18 spare slung under the truck? Rear plate bumper, fridge, drawers, etc, that weighs down the back? If you keep my mother-in-law back there, 44% is NOT enough extra spring rate for that
Pre-loading, as I understand, is a coil-over assembly method. The only thing I think could get messed up when installing the control arms is if the bolts are fully torqued too soon, locking the bushings in a non-neutral position which would lead to them wearing out faster. The same situation must be observed when mounting the coil-over... put the truck on the floor to tighten the bottom bolt so that the bushing sits in a neutral position at normal ride height.
EDIT: Assuming Toytec has an accurate image of an OME90021, it doesn't appear to have any adjustment in the spring perch height. So only a REALLY long spring could be installed on it in a "pre-load" configuration. Which isn't the case, as that the OME 883 is only a tad longer than stock.
Other than that, the suspension moreless goes together only one way.
Glossing over the shocks on Toytec's website and everything seems ok for your setup (assuming you're running stock weight) on the front (OME900021).
However, the OME 60004 rear shocks are valved to match the 895e/895 springs... so they're gonna be stiff as heck.
If it were me, I would choose different rear suspension for on-road comfort. The OME stuff is awesome for off-road, especially for guys with plate bumpers and lots of gear, and you don't need to spend a lot to get it.
Keeping in mind I speak only from looking over the specifications of the info provided. An offroad shop that actually knows how to build things, or a tuning shop that knows suspension, would be able to give solid input. Throwing it on the alignment rack at a place that specializes in alignments may get the specs better... but I don't think it'll effect all the road dip bounce and truck driver up/down stuff very much.
Hope that helps.