Follow the bottom PCB assembly replacement guide then desolder the header completely, and install the parts mentioned in this step.
Though desoldering the header on the bottom board can be much more difficult due to the holes being plated through holes, so it's much more difficult to get the solder out. I used a piece of desoldering braid loaded with solder and a blade soldering tip to heat all joints and remove the header. Very fiddly process.
If you want to experiment you can try snipping the headers short (without disassembling the bottom board) by maybe 2~3mm, and filing the sharp edges down a bit. Though beware of metal dust/clippings that might short out components.
I think it might be fine/preferable to leave/reuse the purple goop between the heatpipe and the topmost shield, as that seems to be quite a bit more spreadable than usual thermal paste used on computers.
For the blue/greyish goop between the heatsink and the SoC shield, and between the SoC shield and the SoC, you might be able to scoop up some of the excess goop that seeped out that are still kinda liquid, and slap it back on to the chip die and copper part of the shield. Though decent thermal paste aren’t all that expensive.