Gamma-ray bursts (GRBs) are flashes of γ-rays thought to originate from rare forms of massive star collapse (long GRBs) or from mergers of compact binaries (short GRBs) containing at least one neutron star (NS). The nature of the postexplosion/postmerger remnant [NS versus black hole (BH)] remains highly debated. In ∼50% of both long and short GRBs, the temporal evolution of the X-ray afterglow that follows the flash of γ-rays is observed to "plateau" on timescales of ∼102-104 s since explosion, possibly signaling the presence of energy injection from a long-lived, highly magnetized NS (magnetar). The cross-correlation algorithm (CoCoA) proposed by Coyne et al. [Phys. Rev. D 93, 104059 (2016)PRVDAQ2470-001010.1103/PhysRevD.93.104059] aims to optimize searches for intermediate-duration (102-104 s) gravitational waves (GWs) from GRB remnants. In this work, we test CoCoA on real data collected with ground-based GW detectors. We further develop the detection statistics on which CoCoA is based to allow for multiwaveform searches spanning a physically motivated parameter space, so as to account for uncertainties in the physical properties of GRB remnants.