Best options to move everything from early 2008 to the newest Mac Pro

I am finally going to make the leap and get a new Mac Pro. Currently on an early 2008 Pro which has been a dream. Zero major problems. I clone my HD to my external Firewire 2TB disk nightly using SuperDuper. Time Machine is also on the external drive as well as a third partition for some miscellaneous storage to free up space on my internal HD.

I am aware that the new Pro doesn't have a Firewire connector but I assume the good folks at my Apple Store can transfer just about everything over for me. I am wondering about consumer products that can allow me to access my Firewire drive from the new machine should I decide to do this myself.

When I get around to moving all that miscellaneous storage I mentioned from my current external drive to the new one I will be getting, is there a way to transfer data from one drive to the other without having to transfer it all using my new internal HD as the go-between?

Also, I am still running Yosemite. Would it be wise to upgrade first to El Capitan before I make the move? Will that matter much?

And should I use an application which deletes all the associated files when you delete an application so I am moving over less junk? Do those work? Is any better than any other for that task?

This all seems like such a daunting task. Anything else I should be considering? I plan to go ask at my Apple Store but I kind of like having some knowledge of it all before I do that. I realize I have asked a lot of questions here. But that's the point of it all.

Thanks for any advice. :-)