You might want to start with a early version of Bitcoin if your looking to make changes.

The later versions are not suitable for a new blockchain.

If you are looking to make changes and mine a new chain I would do so in a VM with older versions of Bitcoin bitcoin-0.10.0.tar.gz is a good one for making altcoins with.  Just be aware the packages used and code DO have security issues so local VM with no internet for the build is advised.

Once you have created your chain and mined some blocks you can then start for forward port the software the real issue is Bitcoin today is just not as suitable a codebase for making new chains.