Au contraire, the cooling system is integral to the CPUs, so what would really matter is that the power supply was adequate (the dual 2.7 may well have shipped with a beefier ps, and the ps is a known point of failure on the G5s), that there are power connections and mounting points on the logic board, and that Apple Service Diagnostics 2.5.8 was run following a successful transplant (an option in ASD is thermal calibration). ASD 2.5.8 is "out there."
Another key concern would be to ensure that the liquid cooling was thoroughly serviced, with gaskets replaced (a must), hoses inspected and fluids renewed (which has to happen if the gaskets are replaced). It is not a trivial task, but there are some good "how to" guides available "out there" as well.