Looking for help with a new rearend.

Cope,
Usually I mock up everything under the car at ride height, set pinion at 1-2* down with the left upper bar. Many will start with 4 bars all equal length then weld the brackets where the are happy with everything aligning. This gives you the same opportunity to make sure you have proper shock and wheelie bar clearance.

Now with that being said, many will weld the 4-link brackets as you described, parallel to housing flange face and be real close. I like to tig, but mig or tig is fine.

The housing ends should be the absolute last thing welded on. Use the Ford 4 bolt new style ends. You have tons of brake options and they use the std 2.5" brake offset.

Measurements: a 9" pinion is mounted 0.970 to the passenger side and 2.25" down from axle centerline when viewing the carrier from the front. Usually you leave about 1.25 to 1.375 as the space between the axles "inside" the spool/diff. If you center the pinion the drivers axle will be 4" shorter than passenger.

Many people will center the housing as it gives plenty of room to weld brackets on both sides and visually looks better from behind the car.

You can center the pinion, center the housing, or run equal length axles.

Good luck.