Typically you'd remove the whole pedal assembly. Disconnect all brake lines (two to the fronts, one for the rears) and the clutch line. You already removed the nuts holding the top end of the pedal box (shared with the column). Then there are two more nuts holding the pedal box onto studs on the firewall.
This work is easier the higher up you can get the car. A set of ramps is good, high up on jack stands is better, a lift is as good as it gets.
The pedal assembly will hang by the supply hoses from the reservoirs. I drain the reservoirs first, then I unbolt them and move them over towards the middle of the cowl. Then I can pull the brake fluid supply hoses over towards the driver's side, out from the cowl into the frunk and push them through the firewall to get a bit of slack. Make a note of what hose goes where so you get them back in the right place.
This is a good time to replace the supply hoses if they are old. Make sure to use hose rated for brake fluid. Fuel hose won't work, PVC won't work etc. Our vendors sell blue cloth braided hose (EPDM?) that works; you can get the same stuff at VW dealers.
I put down a sheet of polyethylene plastic in the footwell before I start, in order to catch brake fluid spills. Home Depot sells rolls of polyethylene sheathing. You should not use PVC / vinyl, as brake fluid seeps right through.
When you go to put things back together again, don't tighten the bolts / nuts holding the cylinders to the pedal box before you have snugged up the brake hard lines. Leaving them loose allows you to wiggle the brake line connecting blocks a bit so that it is easier to get the flare nuts started. I find hat the clutch line is the hardest, as it binds easily. One trick I found is to leave the forward transverse bolt (the one holding the cylinders to the box) loose, and push the rearward one as far over towards the passenger's side as it goes. This will allow the clutch master to pivot on the forward bolt, and you can move it to an angle where it is easier to get the clutch flare nut started.