Thank you for clarifying the motivation of extending the JTAG side. The USB Blaster is using a TCK of 6 MHZ, which isn't that fast, to my opinion. I think the problems are rather related to cable impedance matching, possibly manifesting by a ringing TCK signal.
I recently did some comparative tests with different USB Blaster versions and different cables (original Altera low-impedance flexprint and IDC cable, as used by Terasic). Generally, a moderate length IDC cable (60 cm) works O.K., but shows already some ringing due to the too low TCL driver impedance. The signal quality can be improved by increasing TCK (and optionally other signals driver series resistance).
Interestingsly, this doesn't work on some boards. I found that they had interfering signals that coupled to TCK and generated false clock edges. In this cases, a very low TCK impedance as with the original USB Blaster is preferable.
A 3 m cable has a round-trip delay of about 30 ns, no problem at a 6 MHz TCK. But you should use matched cable impedances and optionally, but most likely not necessary, individual screened signals.
At least, you should have IDC cables with interleaved GND wires. This ends up in a 50 to 70 ohm imdedance for single ended signals, that has to be matched at the respective driver sides (assuming source termination only). As I mentioned previously, it would be helpful to use buffers for both directions near the board JTAG connector.
If TCK speed turns out to be a problem (I don't think so), the 24 MHz crystal oscillator at the USB Blaster may be replaced by e. g. a 12 MHz device. I didn't check, but from my understandig of USB Blaster operation, I assume that it should work.