Hole spacing do 1.5 or 2". Westside spacing sucks imo, too close. I am about to build a massive one and will be going 1" holes on 2" centers.
Pick a hole size that one of the companies with lots of accessories has so you can pick some up later.
Width-go with 48" outside at max, 42" outside min. I am going with 48.
Weight storage go with 24" depth.
Make sure you take into account pressing height.
Use at least 11gauge.
If you are laser cutting the holes, go ahead and get the holes cut on all sides on all members as it allows the most flexibility.
Figure out what kind of pullup bars you want.
Go with a sumo base
Pretty much if you are going custom, spend a lot of time looking at different manufacturers and figure out what you like. I suggest looking at rogue, sorinex, rae crowthers and elite fts. Also go over to bb.com equipment forum and read all the threads on power racks. Read the reviews and see what people like and don't like and implement those ideas. I have learned a ton doing that.