srhmike

When you diffed the client, did you select Remove GM Sprites?

// ID,Sprite_Name,kROName,iROName,LV,HP,SP,EXP,JEXP,Range1,ATK1,ATK2,DEF,MDEF,STR,AGI,VIT,INT,DEX,LUK,Range2,Range3,Scale,Race,Element,Mode,Speed,aDelay,aMotion,dMotion,MEXP,MVP1id,MVP1per,MVP2id,MVP2per,MVP3id,MVP3per,Drop1id,Drop1per,Drop2id,Drop2per,Drop3id,Drop3per,Drop4id,Drop4per,Drop5id,Drop5per,Drop6id,Drop6per,Drop7id,Drop7per,Drop8id,Drop8per,Drop9id,Drop9per,DropCardid,DropCardper Where do you get the info for 
//3599,AB_ARTHUR Because thats what it shows on my mob_db
I reread your post, The custom your adding is missing its kro name and iro name.

Those weird words are supposed to be like that.  The files you downloaded have to be in those "weird" folders.  You change it then things wont work and you'll be back here asking why.

In conf\battle\client.conf packet_ver_flag2: 0x7FFFFFFF
in src\common\mmo.h 
Define the correct packetver with your client that you are using.
#ifndef PACKETVER
#define PACKETVER 20151104 <~~~~change that date
#endif
then on your clientinfo.xml
make sure that its using the correct packetver has in mmo.h
Somewhere the client isnt working with the server.  Double check all those with the client you are using.
<?xml version="1.0" encoding="euc-kr" ?> <clientinfo> <desc>RO Name</desc> <servicetype>america</servicetype> <servertype>primary</servertype> <connection> <display></display> <address></address> <port>6900</port> <version>55</version> <~~~~~~~~~~~here. <langtype>1</langtype> <registrationweb></registrationweb> <loading> <image>loading00.jpg</image> <image>loading01.jpg</image> <image>loading02.jpg</image> <image>loading03.jpg</image> </loading> <yellow> <admin>2000000</admin> <admin>2000001</admin> <admin>2000002</admin> </yellow> </connection> </clientinfo>  

Hmm it doesn't make sense because I just ran it on mine, and it worked fine.
Your SQL query has been executed successfully (Query took 0.0016 sec) CREATE TABLE `clan` ( `clan_id` INT( 11 ) UNSIGNED NOT NULL AUTO_INCREMENT , `name` VARCHAR( 24 ) NOT NULL DEFAULT '', `master` VARCHAR( 24 ) NOT NULL DEFAULT '', `mapname` VARCHAR( 24 ) NOT NULL DEFAULT '', `max_member` SMALLINT( 6 ) UNSIGNED NOT NULL DEFAULT '0', PRIMARY KEY ( `clan_id` ) ) ENGINE = MYISAM AUTO_INCREMENT =5; [ Inline ] [ Edit ] [ Create PHP Code ] Run SQL query/queries on database zodiacbr_rag: Documentation CREATE TABLE `clan` ( `clan_id` int(11) unsigned NOT NULL AUTO_INCREMENT, `name` varchar(24) NOT NULL DEFAULT '', `master` varchar(24) NOT NULL DEFAULT '', `mapname` varchar(24) NOT NULL DEFAULT '', `max_member` smallint(6) unsigned NOT NULL DEFAULT '0', PRIMARY KEY (`clan_id`) ) ENGINE=MyISAM AUTO_INCREMENT=5 Clear [ Delimiter ; ] Show this query here again Retain query box So something is not right.
Apache Version 2.4.23 PHP Version 5.6.28 MySQL Version 5.6.34 That's what I'm running.
Can you take a screen shot of your database, get your mysql version, screenshot of the error?
 
Update- 
Personally I would drop all the ragnarok tables, every single one of them.
Make sure you have the latest rAthena.
Then import item_cash_db, item cash db2, item db, item db re, item db2, item db2re, logs,main,  mob db, mob dbre, mobdb2, mobdb2 re, mob skill db, mob skill db2, mobskilldb2 re, and roulette.  
Dont do any of the upgrades.  And see where that gets you

Sorry for double post but I found it.  It was in a skin folder.  On the custom skin I added, Phieti Renewal Skin.
Ended up actually being 6 different ones in all the custom skins I added.
Why would it load the loading screen from there?

Do what it says, change the permission on the data/logs to 0600