Ultrafast photodriven electron transfer reactions starting from an excited singlet state in an organic donor-acceptor molecule can generate a spin-correlated radical pair (RP) with an initially entangled spin state that may prove useful as a two-qubit pair in quantum information protocols. Here we investigate the effects of modulating electron-nuclear hyperfine coupling by rapidly transferring an electron between two equivalent sites comprising the reduced acceptor of the RP. A covalent electron donor-acceptor molecule including a tetrathiafulvalene (TTF) donor, a 4-aminonaphthalene-1,8-imide (ANI) chromophoric primary acceptor, and an m-xylene bridged cyclophane having two equivalent pyromellitimides (PI2), TTF-ANI-PI2, as a secondary acceptor was synthesized along with an analogous molecule having one pyromellitimide (PI) acceptor, TTF-ANI-PI. Photoexcitation of ANI within each molecule results in sub-nanosecond formation of TTF+•-ANI-PI-• and TTF+•-ANI-PI2-•. The effect of reducing electron-nuclear hyperfine interactions in TTF+•-ANI-PI2-• relative to TTF+•-ANI-PI-• on decoherence of multiple-quantum coherences has been measured by pulse-EPR spectroscopy. This contribution is especially relevant in the absence of modulation of exchange or dipolar interactions, as with the RP at a fixed distance in the molecules in this work. The theoretical prediction of the contribution from an ensemble of hyperfine interactions to decoherence in these RPs is shown to be less than the full width at half-maximum of the quantum beat frequencies measured experimentally. Pulse bandwidth and off-resonant excitation by square microwave pulses are proposed as larger contributors to decoherence in these molecules than the hyperfine interactions, and specific pulse shapes relevant to arbitrary waveform generation are introduced.