Randomizer
In the Plugins folder next to the RanseiLink exe you will see the Randomizer Plugin.
Create Mod
Launch RanseiLink and click the "Create Mod" button

Provide it with unchanged rom, and your desired title, version, author etc.
Click "Create" and your mod should appear in the list.
Randomize
Right click on the mod in the list then in the menu plugins -> randomizer plugin

Edit the configuration, checking what you want to randomize.

Tip
In the randomizer options you will see "Softlock minimization". When checked, various measures are taken to minimize the chances of a softlock, particularly in the tutorial. But there is still no guarantee that you will not run into a softlock.
Hit "Randomize" and it will randomize the data of your mod.
Patch
Finally, to patch the rom, create a copy of your original rom, then right click on the randomized mod
Click "Patch rom with mod" and in the dialog uncheck "Include sprites in patch" since we haven't modified any images so it's unnecessary, and requires extra things to get working. Provide it with the rom you want to patch.

Click "Apply mod" and it will begin patching and notify you soon of completion. Then your rom is ready to go.