Without modification to the code you'd need different ports but my point is not that we want two "identical" blockchain systems as any major problem would presumably hit both of them (i.e. it would be better to have different blockchains that work on different consensus mechanisms).
My concerns with replacing POW and consensus mechanisms are with the following:
Does your new paper contain the advance in technology and knowledge that is needed to produce a truely trusted solution that equals or surpasses the security of proof-of-work and Nakamoto Consensus?