Congrats on a such a big order! Around the holidays, we have this many logo cookies to do. I make lots of dough and icing ahead of time, more than you think you need. I know that one batch of dough will make about 70 2.5 x 3 inch cookies. I know that 100 cookies this size will take a bag of piping consistency and 3-4 bags of flood. I can flood about 80 cookies with all one color in an hour. These all vary depending on the size, colors, design, and shapes. This helps me plan my time.
Then, if they are all different sets, I break down my time to colors and shapes (groups). What colors need to be flooded, what colors would bleed if I did them back to back, etc. I work in groups of what needs to be done first. While I am flooding a first group, my husband is baking the next group. Sometimes I let him flood, after I have outlined. I bought cafeteria trays from Amazon which helps with places to put them as I work. I use a small space heater with a fan to dry them out faster. My entire cookie room becomes a dehydrator by the time I am done! Just be sure not to stack the trays unless you know they will not sag under the heat or weight. I use PVC couplers to put between the trays to elevate them.
A little time organizing yourself will pay off a lot in the long run! Best of luck to you!