What are the steps to customizing a harmonica?

In what order should you do things to make the perfect harp?

I think everyone is a little different and should come up with a checklist that works best for them. With that in mind, here is what I consider best practice:
(use these ideas to make your own checklist)

Always do framework before reedwork. Always complete the reedwork before tuning. Never tune the same day as you do reedwork - unless you are tuning to ET which means you are not looking for precision. Wait as long as it takes. How long depends on how you work the reeds. Start by waiting two weeks. You may need to wait longer.

Framework includes correcting defects, flattening, embossing, etc.... It won't matter that the reed is perfectly straight if the slot is higher on one side than the other or the base of the reed is not centered. By bringing in the edges of the slot, embossing may be useful to help make the frame perfect. For example, some reeds are off-center but that doesn't become noticeable until you emboss. (Don't try to fix an off-center reed with embossing!)

You should be able to do reedwork in one sitting. That is, you set the shape (and gap) of the reed and you are done. That being said, I go back the next day to check my work because I may have missed something the first time around. But it's not because the reeds decided to change shape spontaneously. If you find you need to go back and forth gapping and checking for many sittings before you get it right, I think you should focus on your frame. For example, if you set the reed work relative to the view of the reed from one side but once you put the instrument together, it doesn't perform as expected. You then go back and try setting the shape of the reed relative to the view from the other side. If that doesn't work you try going halfway between both.... Round and round we go! If the frame is perfect and the reed is perfect, no need to fiddle. It will perform as expected whether the plate is on or off the comb, covers on or off. In the long run, this is by far the fastest way to achieve success.

Once it's time to tune, your reeds are perfect and ALL respond the same. This will help you tune. If some reeds need more air than the others, forget about precise tuning. Absolute pitch is never accurate on the harmonica but relative pitch is. Tune notes relative to one another.

Proper tuning technique will not affect the shape of the reed so no need to go back and make corrections to reed shape after you tune. Just like reed work, you should be able to tune to perfection in one sitting. That being said, I go back a little later to check my work because I may have missed something the first time around. Don't check the next day. Reeds can temporarily go sharp. Don't chase your tail. Give yourself a realistic time frame for tuning.

All of these details are explored here:

http://harp.andrewzajac.ca/Learn

I hope that helps.

Andrew