Quickly repeatedly get data out of running system over JTAG/SignalTap/Quartus?

This method would work fine:

http://www.alterawiki.com/wiki/using_the_usb-blaster_as_an_sopc/qsys_avalon-mm_master_tutorial

Use the JTAG-to-Avalon-MM Master. Connect your IMU as an avalon slave, and then use Tcl to read from it. System-Console Tcl works fine.

What I do not like about the Altera tools (and the Xilinx tools) is they do not provide a nice low-level API/DLL/Shared Library that we can link our custom application code with. The work-around is to run a server in System-Console (Altera) or xtclsh (Xilinx) and then just use sockets to communicate from your custom GUI to the hardware. The tutorial contains example server and client code. The JTAG clock rate is around 6MHz, or a bit-rate of 6Mbps. The sustained data rate over JTAG is around 600kbytes/second (about 10 JTAG clocks per byte on average).

Cheers,

Dave