Reference points

There are Multiple diagonal measurements for body alignment, wheelbase checks, rear end centering,and lower BJ location.
The front and rear stub frames are welded in so if the "frame" is tweaked, you can't do much about it except compensate by moving the suspension pick-up points.
As to the front;
The 4-wheel alignment will reveal your Thrust angle, and then you can decide what to do about that, if anything.
The front suspension is built around where the lower BJs end up, so it's kindof important to have them correctly located.
Make sure the front frame rails are in good shape, and that the aprons are well secured, especially at the firewall . The cavity below the Upper A-frame mounts, tend to collect debris and water, and so they end up thin and or holed. You can't have those mounts moving around. The aprons also tend to separate from the upper shock mount. The rear part of the front rails also collect junk and water between it and the floor, and the T-bar sockets occasionally rip out. I guess it would Sux to be you if that happens at speed; I've seen the damage that occurs when that happens just sitting in your driveway.
As to the rear;
You can correct the rear axle alignment if/when you move the springs inboard. The rear spring mounts tend to break out, dropping that corner.
Your rockers on a unibody are structural, and until you install frame connectors, must be in good shape.
Other
The cowl needs an inspection as well, cuz they also collect debris and water, and when they rust out, you get a foot-bath in the rain, and your feet freeze in winter. Water entering from there collects under the carpet in the footwells..... so if your footwells are holed, probably so is the cowl, or the base of the windshield.
On fastback/sportback models, the bottom corners of the rear windows often allow water penetration there, which ends up in the pockets between the rear quarters and the trunk extensions, spelling their death.
The core-support is structural and keeps the front ends of the frame members properly located. and therefore your suspension located. That whole front tub is one large structure and needs to be as good as immovable.
That's all I can think of.