IilyaKol, why did you remove the entire airbox?
When I did the spacer I just took the hose off the TB and removed the TB then took the top of the plenum off. I didn't actually remove the upper plenum itself because I didn't want to install the TB coolant circumventing adapter and didn't want to deal with air in the coolant lines so I held the upper plenum up and out of the way using the mesh pocket from the trunk. Latched one side to the hood strut and the other to the drivers windshield wiper.
BTW this is the optimum opportunity to have your lower plenum ported and polished. You can do it yourself if you feel confident and are handy or have it done at a shop. I did it using a 60 grit sanding wheel

Then a 180 grit sanding wheel
then a nylon brush polishing wheel
If you have the patience and time this entire lower plenum should take you roughly 3-4 hours. I only took enough of the material off to make the runners nice and smooth all the way through. I haven't dyno'd my work but my butt tells me a few HP at the wheels with the port/polish and plenum spacer. Plus after you finish the install and reset the TB, idle and ECU you may notice a much quieter idle. It's so quite for me now that I can't tell if the engine is on from the inside.