Has your full node re-implementation been reviewed? The Core developers usually discourage people from re-implementing the bitcoin protocol as the people fix intentional quirks.
My node has been up and running since last December and has successfully processed the entire block chain starting with the genesis block. Since I do not support mining, I don't see a problem since I don't create new blocks which could cause a fork. The worst that happens is the node refuses to accept a block until I figure out what is causing the problem (the blocks generated by Luke Jr are great for testing the script parser ...)
And yes, I've had to implement the bugs in order to match the reference code.