Thanks for the tips Xavier!
I haven't touched the confluent.metrics.reporter.whitelist config. Setting the confluent.metrics.reporter.max.request.size to 10MB fixed the broker message size issue, so thanks for that!
The corrupt index issue seems to not happen when I use the kafka-server-stop script, as opposed to kill -9, which is what I had previously set up in my /etc/init.d/kafka script. So that issues looks like it is solves as well.
As far as the control center, resetting the control center id worked. This resolved the lock issues and the control center was able to start up cleanly, Getting the GUI back up and running. It still appears to be in a delicate state though. I get the pulsing "Initializing" or "Loading data" dialog, or sometimes the grey loading bars. The UI hangs like this for a very long time, like 20 or 30 minutes. I suppose I'll chalk that up to the command center just taking a long time to initialize? It is spewing out tons of these warnings now:
[2017-04-04 22:27:25,651] WARN Missing sequence numbers=[46, 47] from client=producer-16, topic=XXX, partition=16, estimated timestamp=1490811907492, next timestamp=1490811907492 (io.confluent.controlcenter.streams.verify.MonitoringVerifier:331)
[2017-04-04 22:27:25,652] WARN missing monitoring data for client=producer-16 topic=sf.merch partition=16 session=49f22f37-9b40-4f0c-9e73-3ea372e61d0e window ranges=[[1490811240000?1490811960000]] ClientID=producer-16, topic=XXX, partition=16, session=49f22f37-9b40-4f0c-9e73-3ea372e61d0e, timeout=45000, windowHistorySize=10, shutdownReceived=true, maybeSessionEnded=false, sessionEnded=true, lastSequenceTime=1490811982698, expectedWindowDistance=135000, lastSequenceWithWindow={Sequence=53, Timestamp=1490811982698, minWindow=1490811825000, maxWindow=1490811960000}, Ranges=[] (io.confluent.controlcenter.streams.verify.VerifyTransformerSupplier:445)
[2017-04-04 22:27:25,652] WARN Missing sequence numbers=[1, 4] from client=producer-16, topic=XXX, partition=16, estimated timestamp=1490750343590, next timestamp=1490750343590 (io.confluent.controlcenter.streams.verify.MonitoringVerifier:331)
[2017-04-04 22:27:25,652] WARN No window info in the next non-missing sequence. Estimated window range for missing sequence=6 [1490811015000...1490811135000], lastSequenceWithWindow={Sequence=5, Timestamp=1490750343590, minWindow=1490811045000, maxWindow=1490811105000} for clientId=producer-16, topic=sf.merch, partition=16 (io.confluent.controlcenter.streams.verify.MonitoringVerifier:640)
[2017-04-04 22:27:25,652] WARN missing monitoring data for client=producer-16 topic=sf.merch partition=16 session=d5d8f144-530f-42c6-9eca-e0e82a7fa767 window ranges=[[1490811015000?1490811135000]] ClientID=producer-16, topic=XXX, partition=16, session=d5d8f144-530f-42c6-9eca-e0e82a7fa767, timeout=45000, windowHistorySize=10, shutdownReceived=true, maybeSessionEnded=false, sessionEnded=true, lastSequenceTime=1490750343590, expectedWindowDistance=60000, lastSequenceWithWindow={Sequence=5, Timestamp=1490750343590, minWindow=1490811045000, maxWindow=1490811105000}, Ranges=[] (io.confluent.controlcenter.streams.verify.VerifyTransformerSupplier:445)
Anyways, it's probably an unrelated issue. Thanks for the tips! They were very helpful.