Hi Stillianos,
No, you've got the sequence of steps a bit out of order, though partly correct.
YES, you can start by installing a new server with Windows 2012 R2 and Oracle appropriate version (double-check the PAM to ensure the target Oracle version is ok with ECC 6.0). However, do NOT install SAP onto this new server yet.
Step 2 is the homogeneous system copy from your ERP 6.00 system on Win2003 to your new Win2012 server. Note it will still be ERP 6.00 at this point. You will probably use a newer kernel (7.21_EXT, I think) for the target system, so make sure you choose a kernel that support Win2012 R2, Oracle 11.2, and NetWeaver 7.00.
Step 3 is to upgrade your ERP system by applying EhP6.
Regards,
Matt