The sidebar issues should be resolved in the next build.
Can you provide more info about the indexing issues? What syntax are you dealing with? Does the indexing work with build 3126?
If you open the Help > Indexing Status… window and then save one of the files in the folder, does the indexer queue it for indexing?
There were some changes to syntaxes in 3129, and some users have had issues because they had copied package data over from ST2, effectively overriding the configuration that comes with ST3. Perhaps you could check and see if the indexing works properly in a reverted state? (http://www.sublimetext.com/docs/3/revert.html). Just be sure to move your data folder rather than delete it.