We give a fault tolerant construction for error correction and computation using two punctured quantum Reed-Muller (PQRM) codes. In particular, we consider the $[[127,1,15]]$ self-dual doubly-even code that has transversal Clifford gates (CNOT, H, S) and the triply-even $[[127,1,7]]$ code that has transversal T and CNOT gates. We show that code switching between these codes can be accomplished using Steane error correction. For fault-tolerant ancilla preparation we utilize the low-depth hypercube encoding circuit along with different code automorphism permutations in different ancilla blocks, while decoding is handled by the high-performance classical successive cancellation list decoder. In this way, every logical operation in this universal gate set is amenable to extended rectangle analysis. The CNOT exRec has a failure rate approaching $10^{-9}$ at $10^{-3}$ circuit-level depolarizing noise. Furthermore, we map the PQRM codes to a 2D layout suitable for implementation in arrays of trapped atoms and try to reduce the circuit depth of parallel atom movements in state preparation. The resulting protocol is strictly fault-tolerant for the $[[127,1,7]]$ code and practically fault-tolerant for the $[[127,1,15]]$ code. Moreover, each patch requires a permutation consisting of $7$ sub-hypercube swaps only. These are swaps of rectangular grids in our 2D hypercube layout and can be naturally created with acousto-optic deflectors (AODs). Lastly, we show for the family of $[[2^{2r},{2r\choose r},2^r]]$ QRM codes that the entire logical Clifford group can be achieved using only permutations, transversal gates, and fold-transversal gates.