Ok, I by NO means profess to be a master at Zen Cart or web design or SEO, but have learnt quite a bit in the last month whilst getting this site up and going. If i had started off with list of priority's and order to do this, i would have probably have done this in exactly half the amount of time taken to date.
1- Start of with your SEO in mind first (i think derekjay pointed this out at some point, was a bit late for me, but wish i had, it wasted alot of time) Use his free online course, loads of tips and tricks! Get your key words in order so you can base your domain name, titles etc before you even go! If i had spent 2 days here first, alot of time would have been saved!
2 - Install the Zen cart, make sure its up to date first! Create a back up folder STRAIGHT away on the server where you can just drop the entire contents of the AC folder in every once and a while to maintain a back up. Trust me, it doesn't take alot to crash it and looking around the ZC site for replacement pages files can take ages - rather have copies on your side!
Make those backups OFTEN. Do install SQL patches/installs without backups either
3 - Find your right template FIRST! Get the look of the site in colour and style right before making admin, block, page. logo changes etc. There is a very real chance that you will be redoing delivery php changes, logo changes AGAIN if you change the template later
4 - Try to decide what addons/plugins you want before doing to much also, IE google analytics, sitemap, delivery options, as well. They can also come with there challenges and much easier to do at the start if possible.
5 - List a few products for demo (they do have some) just to learn how it works. Map out your categories on paper, rather more than less. Easy to get rid of them, time consuming to move 20 products from category to another.
6- Build your site at the original address where it will always be. Its made out to be really easy to move... buts it not that easy. 5 hours is what it took, locating new install files that were deleted, changing links manually, database challenges... not so easy.
7 - Before you move to far forward, once layouts etc are done, test in firefox and IE!! Layouts can change enough that it can look terrible
Hope it saves a little time - might seem alot obvious to some, but to me only became obvious half way through!!