This is a very easy technique that allows any amount of Magic Stones after completing Rolling Rapids (level 1) and to do it only requires a bit of time investment and a little setup pre-run.

(Video would go here but I don't want to make one so if someone else makes a video I will put it here)

Basics: By quitting out of a save file and starting a new game when you complete Rolling Rapids and enter Bog Town you will get all the runes from the first save file.

Setting up a Magic Stone Save File: I recommend that you have a save slot dedicated to storing the Stones.

To start, play the game normally and collect as many Stones as you want. (See my list of stone locations for where to get them) I recommend only playing up to Dark Trail Ruins because after there are fewer stones for the time. (Side note: I don't know if the glitch works with a completed game file so yeah don't beat the game) Once you have completed one run of collecting Stones and have finished a level, when you load into the next level quit to the main menu. From the main menu start another run of collecting Stones. Repeat this cycle until you are happy with the number of Stones you have collected. The NOTE: The Stones will not transfer until you load into Bog Town.

Pre-run Setup: Before each run load up your save file with all the Stones like before, quit out, start a new game, and have your Stones to run with. If you are using an emulator you can set a save state after quitting out from your Stone Storing file and just load that State before each run.

Technical: I don't know why it works, maybe something with the way the game loads the levels and reads the old save data?

Glitch discovery: Orcalive (I am pretty sure) Time Save: Untested but a bit Difficulty: 2/10 (time-consuming to farm the Stones but easy execution)