A couple of tips I can think of is;
Establish your vehicle centerline and axle centerline and make all measurements from that.
After the vehicle is level front to back, side to side, Plumb-bob to the floor and mark, from two like points on the front of vehicle and two like points on the rear of vehicle. Make your centerline on floor from these reference points. Transfer the centerline to the vehicle and mark it.
A common laser found in the lumber yards is a big help when transferring the centerline to the vehicle. Make sure you level the laser!
It is a good idea to drill 1/8" holes in several places along the centerline to permanently locate the centerline for future use.
Find center line of the front spindle, usually the lower ball joint grease jerk is damn close as an example. Plumb-bob this to the floor on both sides. Measure back your intended wheelbase with marks on floor, both sides, measure for squareness with front marks and put your axle centerline on the floor. Transfer this to the vehicle with 1/8" holes in a couple of places if you can.
Now you have your vehicle center line and axle center line. Make all measurements from these lines and keep your world square, you will not go wrong.
If you have wheels and tires coming, how did you arrive at the correct back-spacing for the wheels? If these wheels are with the parts you will be getting, it might be easier to get different wheels with different backspacing rather than shorten the housing/axles, etc.