CS PhD application with low GPA but extensive research experience
You need to check the requirements of the individual schools to see if a transfer is even possible. For the German schools, at the very least, the computer science degree is often subject to "continuity" requirements, which make it very difficult to enroll in a master's program unless you already have the bachelor's in the same subject from a German university (or can demonstrate "equivalence" of your degree if it's coming from abroad).

In addition, admission often depends fairly strictly on GPA, at least at the master's level. Recommendations hardly matter, if they even count at all. At the PhD level, the process changes, and becomes more like getting hired for a job. So it may be better to wait until you're applying for PhD positions.