Thoughts and ideas
How nice of you!!
First let's tackle shipping. The way my baker (for my party favor store) ships her cookies and they almost NEVER break is: once she has put them in the cello she then puts each one in a small paper bag 'sleeve' (think of a glassine cookie bag) and basically stands them up/leans them against each other in a box. Then that box is put in another shipping box that has lots of peanuts/bubble wrap in it (this last step is done by a lot of professional bakers - the box inside a box).
That being said, the way I've done it (only twice but with good luck) is to use one shipping box only and use shredded paper as the filler. So first a layer of shredded paper, then the first layer of cookies (laying flat and not touching), then a layer of shredded paper, etc. I used this before when I was sending about 75 of fragile small items I made (as party favors) to a box that I shipped; never had breakage.
Yes - agree with the recipe and royal frosting. I think I would use the royal icing also to do the initials if you decide to do them yourself versus the markers only because the 'raised' initial might look more elegant.
I use a impulse heat sealer to seal my cookies in cello:
http://www.papermart.com/standard-sealers/id=18855?SearchItemNumber=2930100T
it was a great investment (about $65 - I use the small one). Once sealed this way that stay fresh for weeks (at least 3 but even more). To fancy them up I put a label on the back (I use lightweight cardstock to make them/print them, use a 3" card punch to cut out each one, and use a tape runner to adhere to the back). I've also, to fancy them up, left about an inch of the cello bag, above where it is heat sealed, before I cut the rest off. Then I used a two hole punch (found at craft stores - same as the card punch) that is made especially for tying bows to punch holes and then tie a pretty satin ribbon to it. Cut the bag to size before sealing (meaning if you are going to tie with ribbon account for that extra inch before cutting the bags; then seal the cookie.
Timeline: I tend to bake, ice and bag the same day (most cookie decorators don't) because I think you end up with a much fresher product. I often bake/decorate/seal the cookies and then put in the freezer until needed - I've never had a problem with this. I put on the label once thawed.
Hope this helps!
http://s56.photobucket.com/user/Finer_Kitchens/media/cookie%20decorating.jpg