<p>I have an SKR PRO control board with a dead (shorted, it's burning hot) main processor. I ordered a new board, it was my mistake.</p>
<p>The voltage regulators work, so I ordered a replacement STM32F407 processor from STM (a free sample actually) and I'll repair the board in my free time.</p>
<p>How can I test all pins of the new board, so that I can ensure the board is working when I'll sell it/when I'll use it for my next project?</p>
<p>I think that programmatically turning on and off each pin would be enough, then I would use an oscilloscope or a LED to verify the result. The pins which have special functions (heater, fan, MOSFET in general) would be tested accordingly, but I still need the pulsating input.</p>

"Completely" is always relative, but for water at the pressures involved it's probably achievable. Normally you need some sort of
gasket
(material that can bend/compress to slight imperfections in the mating surfaces), and a means of holding the two surfaces tight against the gasket, to get such a seal.
With 3D printing, it's plausible that the print itself could be sufficiently non-rigid to achieve this, if you have a way of keeping the lid and box pressed tightly against each other - bolts through the lid, clips around the edges, etc. But it's unlikely to work well.
I would either print I suitable gasket in TPU, or cut one from some suitable material if you don't have the capability to print with TPU. Either way you still need to design your box and lid so that they're pressed tightly against the gasket.
One possible frame challenge would be doing a round box instead, with a circular threaded lid. It's likely that you could achieve a decent seal for your purposes without any gasket just by tightening the threads, and if not, you still have a really good setup for use with an added gasket.