Often I will leave my office and return to find the fan running at max speed and the computer is unresponsive

I also have a MacPro3,1 (2009) I believe and just started experiencing similar issues as described here.
I have scheduled sleep and start cycles and often I will leave my office and return to find the fan running at max speed and the computer is unresponsive or I find the computer booted in to disk utility mode.
I also often loose ethernet connectivity and have to try renewing DHCP lease several times before it will finally work.
Has anyone found solutions for this. I have looked at the console errors right before shutdown and don't really see anything fishy. Here are the last couple of lines before it looks like it shutdown.
12/4/14 10:08:37.447 PM xpcproxy[5066]: assertion failed: 13F34: xpcproxy + 3438 [D559FC96-E6B1-363A-B850-C7AC9734F210]: 0x2
12/4/14 10:08:58.145 PM mds[38]: (Normal) ImportServer: Ignoring blacklisted Spotlight importer plugin:/Developer/Applications/Xcode.app/Contents/Library/Spotlight/SourceCode. mdimporter uuid:548A3091-3C5D-498A-A329-B532A6C896BB version:1085
12/4/14 10:08:58.193 PM mds[38]: (Normal) ImportServer: Ignoring blacklisted Spotlight importer plugin:/Developer/Applications/Xcode.app/Contents/Library/Spotlight/SourceCode. mdimporter uuid:548A3091-3C5D-498A-A329-B532A6C896BB version:1085
12/4/14 10:08:58.235 PM mds[38]: (Normal) ImportServer: Ignoring blacklisted Spotlight importer plugin:/Developer/Applications/Xcode.app/Contents/Library/Spotlight/SourceCode. mdimporter uuid:548A3091-3C5D-498A-A329-B532A6C896BB version:1085
12/4/14 10:08:58.269 PM mds[38]: (Normal) ImportServer: Ignoring blacklisted Spotlight importer plugin:/Developer/Applications/Xcode.app/Contents/Library/Spotlight/SourceCode. mdimporter uuid:548A3091-3C5D-498A-A329-B532A6C896BB version:1085
12/4/14 10:08:58.301 PM mds[38]: (Normal) ImportServer: Ignoring blacklisted Spotlight importer plugin:/Developer/Applications/Xcode.app/Contents/Library/Spotlight/SourceCode. mdimporter uuid:548A3091-3C5D-498A-A329-B532A6C896BB version:1085
12/4/14 10:08:58.662 PM mds[38]: (Normal) ImportServer: Ignoring blacklisted Spotlight importer plugin:/Developer/Applications/Xcode.app/Contents/Library/Spotlight/SourceCode. mdimporter uuid:548A3091-3C5D-498A-A329-B532A6C896BB version:1085
12/4/14 10:09:57.998 PM mds[38]: (Normal) ImportServer: Ignoring blacklisted Spotlight importer plugin:/Developer/Applications/Xcode.app/Contents/Library/Spotlight/SourceCode. mdimporter uuid:548A3091-3C5D-498A-A329-B532A6C896BB version:1085
12/4/14 10:09:58.142 PM mds[38]: (Normal) ImportServer: Ignoring blacklisted Spotlight importer plugin:/Developer/Applications/Xcode.app/Contents/Library/Spotlight/SourceCode. mdimporter uuid:548A3091-3C5D-498A-A329-B532A6C896BB version:1085
12/4/14 10:10:30.000 PM kernel[0]: PM notification timeout (pid 1514, Messages)
12/4/14 10:10:31.129 PM mDNSResponder[39]: DHCPWakeTime: SCDynamicStoreCopyDHCPInfo index 0 failed CFDateRef start 0000000000000000 CFDataRef lease 0000000000000000 CFDataGetLength(lease) 0
Any help would be greatly appreciated.
<Re-Titled By Host>

Mac Pro early 2009 is Mac Pro4,1, anyway, I think you need to boot into recovery mode, launch Disk Utility, then select startup volume and run repair disk.
Xcode is the latest one, by the way?

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Ollie ...
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