The increased axial coverage of long axial field-of-view (AFOV) PET scanners leads to dramatically higher sensitivity and the potential to significantly reduce scan time and/or radiation dose. Axial gaps allow for longer coverage for a given detector area but have the disadvantages of lower sensitivity and additional complexity for reconstruction. The PennPET Explorer scanner currently has an AFOV of 64 cm with two 7.6-cm axial gaps. We used the system in its current configuration with data gaps and simulations without gaps (70-cm AFOV) to study the impact of large axial gaps on the choices and performance of 3D reconstruction algorithms for long AFOV scanners. The results of this work will inform the extension of the PennPET Explorer beyond 64 cm, guide the development and choice of reconstruction algorithms and parameters for quantitative imaging in long AFOV scanners with gaps, and predict reconstruction performance of longer AFOV systems with and without large axial gaps.