I'm using Solr with Enterprise Edition 1.13. When running a re-index on catalogsearch_fulltext from the command line about 15 minutes into the process the search on the site will start returning an error page with a MySQL error (1205: Lock wait timeout exceeded). Not long after that the indexer.php script dies. Has anyone else run into this problem? Seems like a bug in the core to me. We have not made any modifications associated with search. Running a re-index when using MySQL Fulltext for search works fine.
We had a very similar issue although we're running EE 22.214.171.124. We were getting that same lock wait timeout error from front end searches about 15 minutes in to the Solr reindexing process. Ours eventually did finish though, and after that search would work normally again. In our case Magento support provided a patch which fixed this issue. That patch name was PATCH_SUPEE-817_EE_126.96.36.199. I'd suggest opening a Magento support ticket. Hopefully your issue is the same and they'll have a have patch for EE 1.13 as well.