Smeyers...Go to www.referenceaudiomods.com.
The "basic" mod ($400) would be the usual analog things like Op amps, capacitors, diodes, etc.
Superclock ($295) would affect the digital stuff. The basic power supply changes will also help digital, but they offer a further power supply upgrade ($225) targeted at the DACs.
Finally, for the "ultimate" you get exotic Swiss-made audio transformers, connected directly to the DACs for the outputs, ($600).
If you bought everything the damage would be $1520. Add the cost of the stock Behringer and microphone ($350) and you are up to $1870. But this is still a low cost item in the world of high end audio.
Don't forget that the DEQ2496 sounds darned good in stock form. One consideration which is important for best results is to make sure that the signal level going through the DEQ2496 is high enough to benefit from the 24 bit digital converters. I suggest that users get this right before investing many bucks in modifications. The DEQ2496 has LEDs to indicate input signal level so it easy to tell how you are doing in this regard. The typical home audio power amplifier gain will need to be reduced using its level control, or if it has no level control, by fixed attenuators.