Yeah, it's tricky spot to be in. Beta1 should be out soonish (I forget the exact date, but soon). Then RC after that, or potentially a second beta.
TBH, I would be suuuuper cautious forking and bumping Lucene yourself. Even ignoring the work involved in upgrading from 5.5 to 6.2, you could easily find yourself in a situation where there's an incompatibility between your fork and official ES. Which would put you in a bad spot if/when you want to upgrade, you may have to reindex everything, etc because the incompatibility is not upgradeable.
At that point, you'd be "safer" running off alpha or beta.
What kind of problems are you running into? I think it'd be much easier to work around the query_string quirks. E.g. identify the problematic fields and exclude them from querying via query_string, and instead add extra, specific queries against those fields in a big
bool. Or use a