Interfacing to sld_hub

There are two internal features in 12.1 which might solve your problems.

The first is a direct solution to your problem - instantiate an altera_soft_core_jtag_io module within your alternative controller. The sld hub will be connected to the tck/tms/tdi/tdo pins on the jtag io module instead of being connected to the JTAG pins.

The second is basically SignalTap over TCP. Attach an altera_sld_hub_controller_system to a Nios II (or similar) processor, route data from a TCP connection into the hub controller and set up Quartus correctly and then the Altera tools will talk to SignalTap (and In-System-Sources-and-Probes) over the TCP connection. This will be fully released in 13.0 (I hope) but if you want the reference design and instructions then send me a personal message with your email address. It doesn't have to be TCP for the last few mm - any 8 bit clean bidirectional pipe can be used with a bit of effort.

There is no official support on either feature but I'm sure you can make them work.