Hi,
Ideally you would have an FPGA to passively observe the JTAG traffic and issue a trigger to your ChipWhisperer at or around the “right time”.
But all you really need is a constant time reference that you can use to time your glitch, since you can offset and sweep from there with the ChipWhisperer. I’m not sure what’s the simplest way to do that, I’m just pointing you in (hopefully) the right direction.
One option is to adapt our PhyWhisperer-USB for your purposes, as explained here.
You might also get some ideas from Dmitry’s bootloader bypass tutorial.
Jean-Pierre