If the forks are not extending completely then the cartridge has air in it. The way the Marzocchi 48 fork works it has probably pumped out too much oil from the cartridge, and in to the main chamber, and needs to be redone. To get the nut off the lower fork leg quickly and easily I recommend hitting it with an impact gun. I did a complete video on breaking down these forks and hope it can be of some help. If it does, please give it a thumbs up on Youtube.
https://youtu.be/dbKjhvFl7AQ
As for the shock. Top is always compression and bottom is rebound. Also, the big nut around the compression adjuster is normally the high speed compression adjustment. I recommend full open (CCW) and then turn back in 1/16 to 1/8th (a little is a lot!) of a turn for most off road type riding and more (1/8 to 1/4 turn in) for high speed whooped out or MX tracks. As for the others, set to middle positions and then slowly dial them in one at a time. There are plenty of online guides to get you going in the right direction.
Also, and most importantly, make sure you have the correct springs for your weight installed front and rear and that your sag is set within the correct range. Sag can totally change the way a bike handles with only a 1mm change.