This vid covers how to test the fan circuit itself.
vw Golf mk4 fan switch check climatronic fan check guide - YouTube
With IGN off you can get low speed, with IGN on you can get High speed.
If this test works OK your fans and the last part of the circuit is OK.
If they pulse when in high speed mode you may have an issue with the fan itself.
What is the frequency of the pulsing ? High for how long ? low for how long?
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