- I will replace the valves with original spares, do I also need to change guides and springs?

Yes on the guides.
If the springs are in spec I would re-use them.

- I am thinking of machining the cylinder head in order to increase the compression ratio. What are the pros and cons, assuming everything is calculated and done right? (mechanical engineer here)

Recommend against because of the tolerances between the moving parts of the block/head. You got 300k+ out of what you have - why not stick with it? (mechanical engineer here)

- I obtained mahle pistons with +0.05mm diameter. In order to insure longest engine life and less compression leak, what is the optimum honing value recommended for the cylinders? I will make sure the engine is treated carefully during the break in period anyways so I want to go as tight as I can.

I would follow the specs in the manual on this one.

- How exactly are pistons and rods blueprinted? Do you recommend material removal in order to make all parts weigh same?

I recommend against material removal unless you are building a race car.

- What is your recommendation for the crankshaft?

Let the machine shop inspect the crank. Best case all they will do is polish it. Worst case they will have to turn it some and install oversize brgs.
good luck

__________________
Jim