Accessing JTAG pins using Virtual JTAG Megafunction

I don't exactly understand, what you are trying to achieve.The VJTAG MegaFunction doesn't give access to the JTAG pins rather than to the nodes of the virtual JTAG hub, as discussed in the VJTAG user manual. TDO output is only routed according to the state of the virtual JTAG state machine, during an active VIR/VDR scan.

I agree, that it would be good to have more virtual JTAG details documented by Altera, e.g. the operation of VJTAG instance types used by Quartus as SFL and SFL enhanced, or the sld_hapi software interface. The SFL operation is rather low level, directly shifting data in and out of the serial flash, as far as I remember. You should be able to extract the VJTAG codes from the alt_sfl.vhd respectively alt_sfl_enhanced.vhd code in quartus/libraries/megafunctions.