I was able to locate the mongod.lock file on a different drive. I performed the steps mentioned and removed the lock file (1KB in size). On splunk restart a new one was created that is 0kb. However I am still receiving the "Key value store must be enabled. Please enable it" in splunk. I re-traced my steps and will paste the mongod.log file below. It appears to me that there is a potential permissions issue with the file. Our splunkd service runs as a local system account. I found some linux articles when searching for the specific errors but nothing that seemed relevant. New log pasted below broken up by steps I had taken.
2015-08-13T17:40:17.665Z warning: No SSL certificate validation can be performed since no CA file has been provided; please specify an sslCAFile parameter
2015-08-13T17:40:17.949Z [initandlisten] MongoDB starting : pid=1732 port=8191 dbpath=D:\Splunk\var\lib\splunk/kvstore\mongo 64-bit host=SAC-CORP-SPLKH1
2015-08-13T17:40:17.949Z [initandlisten] targetMinOS: Windows 7/Windows Server 2008 R2
2015-08-13T17:40:17.949Z [initandlisten] db version v2.6.7-splunk
2015-08-13T17:40:17.949Z [initandlisten] git version: 7e66fa196686092ee1c184bd3f8fa1fe640c6550
2015-08-13T17:40:17.949Z [initandlisten] OpenSSL version: OpenSSL 1.0.1m-fips 19 Mar 2015
2015-08-13T17:40:17.949Z [initandlisten] build info: windows sys.getwindowsversion(major=6, minor=1, build=7601, platform=2, service_pack='Service Pack 1') BOOST_LIB_VERSION=1_49
2015-08-13T17:40:17.949Z [initandlisten] allocator: system
2015-08-13T17:40:17.949Z [initandlisten] options: { net: { port: 8191, ssl: { PEMKeyFile: "C:\Program Files\Splunk\etc\auth\server.pem", PEMKeyPassword: "", mode: "preferSSL" } }, replication: { oplogSizeMB: 1000 }, security: { keyFile: "D:\Splunk\var\lib\splunk/kvstore\mongo\splunk.key" }, setParameter: { enableLocalhostAuthBypass: "0" }, storage: { dbPath: "D:\Splunk\var\lib\splunk/kvstore\mongo", smallFiles: true }, systemLog: { timeStampFormat: "iso8601-utc" } }
2015-08-13T17:40:17.996Z [initandlisten] journal dir=D:\Splunk\var\lib\splunk/kvstore\mongo\journal
2015-08-13T17:40:17.996Z [initandlisten] recover : no journal files present, no recovery needed
2015-08-13T17:40:18.437Z [initandlisten] info preallocateIsFaster couldn't run due to: couldn't open file D:\Splunk\var\lib\splunk/kvstore\mongo\journal\tempLatencyTest for writing errno:5 Access is denied.; returning false
2015-08-13T17:40:19.004Z [FileAllocator] allocating new datafile D:\Splunk\var\lib\splunk/kvstore\mongo\s_splunkiTR2RCAYp7Go4kZlq1TnMAm9_tSessiV6ysHGNENqOVEZL92qEHLjZQ.0, filling with zeroes...
2015-08-13T17:40:19.004Z [FileAllocator] creating directory D:\Splunk\var\lib\splunk/kvstore\mongo_tmp
2015-08-13T17:40:19.004Z [FileAllocator] FileAllocator: couldn't create D:\Splunk\var\lib\splunk/kvstore\mongo\s_splunkiTR2RCAYp7Go4kZlq1TnMAm9_tSessiV6ysHGNENqOVEZL92qEHLjZQ.0 (D:\Splunk\var\lib\splunk/kvstore\mongo_tmp\1439487618012241) errno:5 Access is denied.
2015-08-13T17:40:19.004Z [FileAllocator] error: failed to allocate new file: D:\Splunk\var\lib\splunk/kvstore\mongo\s_splunkiTR2RCAYp7Go4kZlq1TnMAm9_tSessiV6ysHGNENqOVEZL92qEHLjZQ.0 size: 16777216 . will try again in 10 seconds
2015-08-13T17:40:29.090Z [initandlisten] Assertion: 12520:new file allocation failure
2015-08-13T17:40:29.201Z [FileAllocator] allocating new datafile D:\Splunk\var\lib\splunk/kvstore\mongo\s_splunkiTR2RCAYp7Go4kZlq1TnMAm9_tSessiV6ysHGNENqOVEZL92qEHLjZQ.0, filling with zeroes...
2015-08-13T17:40:29.201Z [FileAllocator] FileAllocator: couldn't create D:\Splunk\var\lib\splunk/kvstore\mongo\s_splunkiTR2RCAYp7Go4kZlq1TnMAm9_tSessiV6ysHGNENqOVEZL92qEHLjZQ.0 (D:\Splunk\var\lib\splunk/kvstore\mongo_tmp\1439487618012242) errno:5 Access is denied.
2015-08-13T17:40:29.201Z [FileAllocator] error: failed to allocate new file: D:\Splunk\var\lib\splunk/kvstore\mongo\s_splunkiTR2RCAYp7Go4kZlq1TnMAm9_tSessiV6ysHGNENqOVEZL92qEHLjZQ.0 size: 16777216 . will try again in 10 seconds
2015-08-13T17:40:29.295Z [initandlisten] exception in initAndListen: 12520 new file allocation failure, terminating
2015-08-13T17:40:29.295Z [initandlisten] dbexit:
2015-08-13T17:40:29.295Z [initandlisten] shutdown: going to close listening sockets...
2015-08-13T17:40:29.295Z [initandlisten] shutdown: going to flush diaglog...
2015-08-13T17:40:29.295Z [initandlisten] shutdown: going to close sockets...
2015-08-13T17:40:29.295Z [initandlisten] shutdown: waiting for fs preallocator...
2015-08-13T17:40:29.295Z [initandlisten] shutdown: lock for final commit...
2015-08-13T17:40:29.295Z [initandlisten] shutdown: final commit...
2015-08-13T17:40:29.295Z [initandlisten] shutdown: closing all files...
2015-08-13T17:40:29.295Z [initandlisten] closeAllFiles() finished
2015-08-13T17:40:29.295Z [initandlisten] journalCleanup...
2015-08-13T17:40:29.295Z [initandlisten] removeJournalFiles
2015-08-13T17:40:29.311Z [initandlisten] shutdown: removing fs lock...
2015-08-13T17:40:29.311Z [initandlisten] dbexit: really exiting now
---- After another restart of splunkd -----
2015-08-13T17:50:00.728Z warning: No SSL certificate validation can be performed since no CA file has been provided; please specify an sslCAFile parameter
2015-08-13T17:50:00.932Z [initandlisten] MongoDB starting : pid=6604 port=8191 dbpath=D:\Splunk\var\lib\splunk/kvstore\mongo 64-bit host=SAC-CORP-SPLKH1
2015-08-13T17:50:00.932Z [initandlisten] targetMinOS: Windows 7/Windows Server 2008 R2
2015-08-13T17:50:00.932Z [initandlisten] db version v2.6.7-splunk
2015-08-13T17:50:00.932Z [initandlisten] git version: 7e66fa196686092ee1c184bd3f8fa1fe640c6550
2015-08-13T17:50:00.932Z [initandlisten] OpenSSL version: OpenSSL 1.0.1m-fips 19 Mar 2015
2015-08-13T17:50:00.932Z [initandlisten] build info: windows sys.getwindowsversion(major=6, minor=1, build=7601, platform=2, service_pack='Service Pack 1') BOOST_LIB_VERSION=1_49
2015-08-13T17:50:00.932Z [initandlisten] allocator: system
2015-08-13T17:50:00.932Z [initandlisten] options: { net: { port: 8191, ssl: { PEMKeyFile: "C:\Program Files\Splunk\etc\auth\server.pem", PEMKeyPassword: "", mode: "preferSSL" } }, replication: { oplogSizeMB: 1000 }, security: { keyFile: "D:\Splunk\var\lib\splunk/kvstore\mongo\splunk.key" }, setParameter: { enableLocalhostAuthBypass: "0" }, storage: { dbPath: "D:\Splunk\var\lib\splunk/kvstore\mongo", smallFiles: true }, systemLog: { timeStampFormat: "iso8601-utc" } }
2015-08-13T17:50:00.963Z [initandlisten] exception in initAndListen: 13627 Unable to create/open lock file: D:\Splunk\var\lib\splunk/kvstore\mongo\mongod.lock Access is denied.. Is a mongod instance already running?, terminating
2015-08-13T17:50:00.963Z [initandlisten] dbexit:
2015-08-13T17:50:00.963Z [initandlisten] shutdown: going to close listening sockets...
2015-08-13T17:50:00.963Z [initandlisten] shutdown: going to flush diaglog...
2015-08-13T17:50:00.963Z [initandlisten] shutdown: going to close sockets...
2015-08-13T17:50:00.963Z [initandlisten] shutdown: waiting for fs preallocator...
2015-08-13T17:50:00.963Z [initandlisten] shutdown: lock for final commit...
2015-08-13T17:50:00.963Z [initandlisten] shutdown: final commit...
2015-08-13T17:50:00.963Z [initandlisten] shutdown: closing all files...
2015-08-13T17:50:00.963Z [initandlisten] closeAllFiles() finished
2015-08-13T17:50:00.963Z [initandlisten] dbexit: really exiting now
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