both holes are from interstitial space between water pump transmission oil side and coolant side. This will become apparent when you have disassembled the water pump. if either seal leaks then oil or coolant will weep out. though I do not understand why there are two holes. seems redundant. so yes, cover them with tape before you give the engine a good clean. and post some pictures!
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MC21R9N track
MC18R2J track
CBR954
CR250