First, go to Beta Centauri and mine all the moons. The moons there have 48 of all three items and the respawn rate is very high, allowing you to easily fill your cargo holds relatively quickly. Then, go somewhere that will buy your cargo and sell everything. It is recommended that you have all your Psi so the patrols do not nail you for having Contraband. If you successfully fulfill all three counts, you will get 192 of each item. If you are looking for specific items that you need for crafting, the ones available at Beta Centauri are as follows: Food, Polymers, Minerals, Alloys, Technology, Isotopes, Crystals, Gold, and Contraband (everything except Medicine).
Always work from the outside to the inside on the perimeter to avoid large shifting of gems. This will prevent cascades, which cost time to recover from. Do not go out of your way for clock matches. Try to incorporate them into shifts that you have to do anyway to get the target pieces you need in place. Start grouping clocks in the same area and they will match on their own without you having to take extra time to align them. Always look at the next color gem to save time when scanning for its location.