Well, in terms of an upload script, I would recommend EZUpload Pro. We have 2 clients running it, both publishing houses/print designers, and they are both very happy with it. Note, you will need to modify the max upload size in your php.ini but that's no biggie.
Sounds to me like you are looking much more for a project manager than a support system. Have you looked at the paid Basecamp? To get time tracking you will need to do the $49/month package, but, Basecamp is also a professional-looking and professional-working system. If you take your business seriously and you want the whole thing looking right, working right, under one roof, IMO Basecamp would be a great way to go.
If you can do a stand-alone time tracking system (like on your PC...personally, I use Studiometry, but it's an OS X-only package) then you could get by with a cheaper Basecamp, $12-24/month depending on your project volume.
I'm sure there are other solutions, but if I needed the same set of features, rather than hassle with my own script installations and patching and skinning, etc., I would just outsource the job to Basecamp. They do it right, it looks sharp, and it works.
Let's Connect on Twitter! @thatsmsgeek2u||Fighting mediocrity one thread at a time.
8.8 mb (zip)
Download Studiometry 4.0.3
BuyHTTP Internet Services - In business since 2003 Business Hosting | nginx, CloudLinux, Varnish cache, and CDP with every business account
Shared, Reseller, Semi Dedicated, VPS, Cloud, Dedicated - We can grow with you
I'm curious about the solution you find to your problem. I do hosting, not webdesing, but I have encountered similar requests from my customer base. And I have not been able to give definitive answer, but just recommend a set of tools. Not ideal...
So, if you get something close to what you describe and want to post here, it could be great. Or just drop me an bump and we can complain together about this missing piece
bithost, I will have to check that basecamp. But upfront, from the website, seems a bit too overkilling, isn't it? For just uploading things, I mean.