For this realm, you'll be coming here even if you hit 200k-300k for upgrading your first realm trait Sacred Mirror, it is also a good source of b-tads once you dominate the realm completely.
Intel
Check the images below for cell number context
For Yamato Intel
Ninja Training (4) releases the second skill tree, so this is a good place to start. Chrysanth & Sword (2) unlocks new card conversions, so this is also recommended early on. Get the new areas (middle row) as soon as possible. Ninjutsu (5, 6, 7, 8) is recommended early, as it will help to level up Ninjutsu much faster. Genji (13) unlocks important gear that will assist your Yamato explorations. Finally, Musashi's Legacy (16) has a chance to give the green relic Niten Ichi Ryu, which is necessary to complete the Yamato Domain.
For Ninja Training
Stealth (2) will increase movement SPD and lower AFFCT Checks, so this is a great first tile to get. Ninja's Gesture (4) will increase Ninjutsu Training SPD and help to max it out much faster if obtained early. Ninjutsu training (15, 16, 18, 19) will also assist with this. Kani Jade (13) gives plenty of fragments to upgrade this relic, and will be a great display item in the Museum. Finally, Divine Retribution (11) increases DMG done in Yamato. Scared Mirror (17) will be your first realm trait and a KEY gameplay item to get ASAP. You'll be using this 99% of your game time even in future realms.
Cards
YOU SHOULD GET THE ENERGY CORE CARD FIRST! LET IT BE IDLE WHILE YOU WORK ON THE OTHER CARDS!
Recommended Cards to get FIRST are:
White - Enhancement Injections, Gear, Underground Explorer
Green - Enhancement Injections, Gear, INTEL
Blue - Enhancement Injections, Gear, Energy Core
Purple - Enhancement Injections, Gear, INTEL
Orange - Enhancement Injections
Ninjutsu
Ninjutsu is the unique mechanic in Yamato and has four types: Fire, Aqua, Thunder, and Earth. Each type corresponds to one of the Snail's HARD stats.
By hitting the grids relating to Ninjutsu, durng exploration, you can acquire the necessary points for upgrading each type.
The recommended order is Fire > Thunder > Earth > Aqua. Practice these in order first as they will help increase the leveling.
Now the biggest part is the techniques. Clearing each of the techniques (five points per technique) will reward you with Mirror Fragments.
To get fragments quickly, i recommend you do each ninjutsu first skill then second and third as they will increase in Chakra cost.
Don't spend your intel on anything that is NOT recommended above. Use it on chakra, 10 intel = 1 chakra.
You're ultimate goal is to max out your sacred mirror.