Ok man, I've taken a look at your files and found a few issues.
For base building, the reason you aren't publishing to the database is because you somehow have an extra
on line 13 of dayz_server\compile\server_publishObject.sqf
Your RPT is getting spam about "message type null" or something like that. That's coming from your custom monitor, move the call for it in init.sqf away from the bottom and into the dedicated section.
Just after your refuel script call.
Also, there is a little problem I only just found out about whilst checking your files. The custom loot setup needs some additional files edited.
dayz_server\compile\fa_hiveMaintenance.sqf
dayz_server\compile\fn_bases.sqf
dayz_server\compile\server_spawnCrashSite.sqf
Each of them has one reference to configFile loot something or other. Do the missionconfigFile change for all instances pointing to a loot file. Seems this problem is only apparent if you've edited the loot tables for heli crashes, castles and something else I can't figure out haha.
Your mission file is also almost double the size it needs to be because you have .bak copies of almost all the files in there. Really you shouldn't keep them in the mission folder because it's just increasing the mission file size for no reason.
Another thing, you've got two fn_selfActions.sqf. One being called right after the other. It looks like one was for Kirxes' self blood script and the other is the one I included with the BB edits in. You've already added Krixes' stuff to the BB one, so you can remove these files
missionfolder\scripts\fn_selfActions.sqf
missionfolder\scripts\compiles.sqf
Then remove this line from your init.sqf
Code:
call compile preprocessFileLineNumbers "Scripts\compiles.sqf"; //Compile custom compiles
Sorry if that's a bit long man, figured I may as well take a crack at the other issues showing in your RPT whilst I was at it.