I found an effective way to get rid of huge Ikko-Ikki stacks, and in short is called 'prevent them from refill their ranks'. Do as follows:
-Raise levies to gain at least a total of 1.5 to 2 times their numbers
-Split them into several stacks of 10-12k depending on the enemy numbers (you should always have a number greater than 10k)
-Put all your divided stacks onto province bordering the Ikko-Ikki
-Engage, carefully, one stack, as soon as you are about to have it wiped out make him retreat and move the 2nd stack and make sure it arrives before the end of the month.
-Engage with all stacks, when the last one has been forced to retreat, send again the 1st, that should have recovered morale if not numbers.
-Rinse and repeat the engagements.
Basically, all you are doing is to 'defeat them thanks to low morale'. If you never allow them to begin a new month while not fighting, they will not gain troops and will not gain morale, meaning that after 2-3 engagements they will do no damage.
The '10k' minimum is to make sure you always cover all the front line and make all of them lose morale and become 'unfilled' single infantry units (only the front line fights, so you have to make sure they cannot always field a full line with full numbers and morale).
Being all infantry, every shock phase is where you see if you are effectively lowering their numbers, as they have no cavalry (a good general leading a late engagement with a lot of cavs will make wonders, ofc).
Good luck, lemme know how it turns out

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