3 thoughts come immediately to mind. Shot seals in the master cylinder that allow for fluid to "bleed back" vs pressurizing the system. Air trapped in the system (ABS is the usual suspect, but you need software and a late 99+ or to be able to lock up the brakes). The third is that some people have encountered this before with the TBU and Never figured it out.

If the brakes were working fine (pedal travel/feel) before the TBU upgrade, it's almost certainly air in the system. Time to go to each junction point with a rag, helper on the pedal as you crack it free and do a 1-pump bleed from each, and every, connection in the brake system. Air likes to hold on at junction points, this is the fastest way to resolve it. Pressure bleeding with air already in the system just leads to cavitation/breaking up of the air and doesn't usually resolve the problem (at least in my experiences). I'd probably leave the ABS pieces till last, just to see if I could get the ABS to kick on after doing the rest.

You could also try parking on a Steep incline overnight and tapping all the lines before leaving it. Might help the air brake free and migrate to the highest point (nose up, obviously). Might also do nothing... used to work well on motorcycles, next morning would always find a good bit of air at the banjo bolt for the master cylinder.