Sorry, I don't know the meaning of your plots, but here a reworking that runs:
Clear[TF1, inwave, coupling, v1];
PulseWave[duty_, t_, period_, phase_] :=
UnitBox[Mod[(t/period) + phase, 1]/(2 duty)];
TF1 = TransferFunctionModel[{{(697052. + 25694.6 s)/(700128. +
25835.5 s + 1. s^2)}}, s, SamplingPeriod -> None,
SystemsModelLabels -> None];
inwave[t_] =
OutputResponse[TF1,
40*10^-3 PulseWave[0.25, t, 10^-3, 0], {t, 0, 4 10^-3}][[1]];
Plot[inwave[t], {t, 0, 4 10^-3}, PlotLegends -> {"inwave"}]
coupling[t_] = OutputResponse[TF1, inwave[t], {t, 0, 4 10^-3}][[1]];
Plot[{coupling[t], inwave[t]}, {t, 0, 4 10^-3}, PlotRange -> All,
GridLines -> {{}, {.015}}, PlotLegends -> {"coupling", "inwave"}]
v1[t_] = If[coupling[t] >= 0.02, inwave[t], 0];
Plot[v1[t], {t, 0, 4 10^-3}, PlotRange -> {-.01, .045},
GridLines -> {{}, {.015}}, PlotLegends -> {"v1"}]