Please excuse my ignorance, but I don't know what you mean by colour coding my files?
I have quite a few files, I've never counted.. but it's getting up there. I haven't had any issues yet findings things using specific patterns. Even on the client side I'm following an MVCish type structure.
I generally start my base structure off with the top level folders o
client
collections (sit outside and just wrap the necessary stuff in Meteor.isClient/isServer as I've had some issues with pubs/subs not working correctly when nesting them in the client/server folders)
server
inside client I have my views, helpers, controllers, and a single router.js file. Sometimes i'll have an index.js in the root of my client folder for any startup or very client specific stuff that doesn't relate to a controller or view or helper etc.
inside my views I break it up by resource, so clients, products etc.. in each I follow a crud naming convention. index, new, edit, delete. And for each view I have a js file for it's events etc. I had those separated at first, but it didn't feel right and was harder to navigate.
In server, I just have the index.js for server specific things, email templates (I use a meteor method or observe collections to send out emails automatically server side).
Right or wrong (no idea as there doesn't seem to be a standard yet?), it's working for me so far. I've switched it up here and there and it's a continual learning experience. I try to find blog posts or other snippets from people about how they structure their meteor apps.