The original FlexiChain and its descendants are a revolutionary distributed ledger technology (DLT) for cyber-physical systems (CPS) and their embedded systems (ES). FlexiChain, a DLT implementation, uses cryptography, distributed ledgers, peer-to-peer communications, scalable networks, and consensus. FlexiChain facilitates data structure agreements. This thesis offers a Block Directed Acyclic Graph (BDAG) architecture to link blocks to their forerunners to speed up validation. These data blocks are securely linked. This dissertation introduces Proof of Rapid Authentication, a novel consensus algorithm. This innovative method uses a distributed file to safely store a unique identifier (UID) based on node attributes to verify two blocks faster. This study also addresses CPS hardware security. A system of interconnected, user-unique identifiers allows each block's history to be monitored. This maintains each transaction and the validators who checked the block to ensure trustworthiness and honesty. We constructed a digital version that stays in sync with the distributed ledger as all nodes are linked by a NodeChain. The ledger is distributed without compromising node autonomy. Moreover, FlexiChain Layer 0 distributed ledger is also introduced and can connect and validate Layer 1 blockchains. This project produced a DAG-based blockchain integration platform with hardware security. The results illustrate a practical technique for creating a system depending on diverse applications' needs. This research's design and execution showed faster authentication, less cost, less complexity, greater scalability, higher interoperability, and reduced power consumption.