interesting layout. I use teleport pipes and diamond pipe to create something similar. The center of my system is a backbone looking construct of pipes: teleport in -> gold -> diamond -> 2x stone -> diamond ->2x stone -> diamond -> 2x stone - diamond -> teleport out to mass storage/default chest. Off of each diamond pipe can be up to 4 teleport pipes going to different machine rooms. Machine rooms have 2 sets of pipes. The input teleport->gold->N x insertion -> teleport to mass storage for overflow. Then there is a output line that redirects back to the start of the backbone. Since everything goes through that main backbone line it makes a good way to monitor how mining is doing.
I think I need to do some screen shots.
I only like to use the TP pipes for long distance stuff (where you HAVE to use them due to the way the game works). Feels too much like cheating (IMO) otherwise.
The main limitation that I see with doing it the way you are is that a certain item is always handled the same way, whereas with the sorting machines, you can handle the same item differently depending on where it's coming from. In my case, cobble overflowing from storage gets sent to a factory, and cobble coming out of there goes to be macerated (through the same tubes). Plus with the manual input you can send the same item to more than one place - for example, cobble needs to be able to end up in a macerator or a furnace.
Granted, none of this is possible to implement until IC is updated to MC1.0, so what you've got is probably the best you can do right now