Those are rock pits. Look at your windshield at an angle. Bet you have the same thing there. What you did when you polished with XMT is remove all waxes and dirt in the pits. This now has brought them into sight. You might want to try Megs #7 Glaze before waxing.
Remember, the PC can only correct so much. Wetsanding and a rotary may be in order next but these are for a bodyshop's professional.
Don't get discouraged. I have to even stop sometimes and say enough is enough. You can only do so much. I think the paint looks good.
As far as for 3 hours, that seems long. XMT should be used at a #5 setting for about 5 minutes in ideal conditions. I break the hood into4 sections, making sure to overlap. I time myself with a timer to make sure it all comes out evenly. So that's 20 for XMT2 and 20 for XMT1 totalling 40 minutes plus another 10 for pad clean and bottle shaking......let's make it an even hour on the hood. XMT Glaze should be used on a speed no higher than #5 on the PC. I use a #4 personally, doing the whole hood at one time. A quarter sized amount will do the hood. Takes me about 5 minutes to massage the glaze into the paint until it goes a little clear. I buff right off by hand. This gives me about an hour 15 minutes on the hood.
Hope this helps.