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I think this is because you haven't installed the DynDOLOD mod properly yet (at the end of the guide).

To put it very simple: the patches allow multiple mods with conflicting edits to the game to work properly with each other.
 
I'd say that you definitely want to to consider using the 1.D.1 and 1.D.2 settings.  The other settings in the Skyrim Configuration Settings Guide are proceeded by a note: "Notice: The STEP Guide DOES NOT officially recommend all of the following settings, but rather that all of the following INI entries are valid. These settings may improve the user experience, but each setting will be system/environment dependent. The values indicated are usually best for the "Recommended System"."

First of all, when you are creating the merge of the weapons, I'm assuming that you are only merging the 13 intended .esps and not the other 5 DLC .esps also (since you can select those too, undesirably).
 
I just fixed the merging instructions after I redid my own merge of the mods.  Thank you for pointing out the 1>6 number issue - the number was off.  In addition to this, I did in fact find an error line under CrossbowForms to remove as well.  After doing all of this the game loaded fine, so I don't know what is wrong with your setup.

Green = STEP Core mods.  Non-green = STEP Extended mods.
 
You can ignore texture mods if you like, because if you use any of the STEP Patches, those will be only requiring certain plugins (.esps) from mods to work - not textures.  But, if you don't install the texture mods as in the guide your end result will not quite look as intended by the guide.
 
Baseline versus not baseline usually means the difference between choosing a texture mod that uses 1k quality textures versus an alternative for the mod that uses 2k textures (or lower or higher, depending).  The alternatives would be signified by "LQ" and "HQ" symbols.
 
Most of this is explained in the guide itself - the legend, btw.

I think this has to do with using the windowed mode option in enblocal.ini (which is the same file you use to set up ENBoost).  If you are using windowed mode, the in-game brightness settings will not work and you will be forced to use the normal (middle) brightness setting.
 
EDIT: You can get by this by altering your gamma settings for your video card, of course, this will also affect everything else outside the game as well, so you'll have to do a lot of back and forth on that setting when you go from playing Skyrim to not playing Skyrim.

I think you should look over your .ini files to make sure you have the correct settings in them.  Maybe you didn't set things right.  It's easy to mess those .inis up by accident or by not noticing something that should be set differently. 

Apparently, it was in my DDSOpted Textures.bsa files. I DDSOpted them before and had a drive failure a while back, while I was transferring my data from old drive to backup drive the messed up drive kept failing sometimes partway through file transfers. I thought I was able to safety complete all transfers, but perhaps some files got corrupted by being incompletely transferred without me realizing it. I am re-DDSOpting the Textures.bsa files and hopefully that resolves the problem. I also hope that I don't run into other corrupted files as well (like in the other Vanilla BSA files that I previously DDSOpted. I don't want to have to run them ALL through the DDSOpt process again because it takes a LONG time to process them, even with a SSD.
 
EDIT: It did resolve the problem. No more boiled lobster-faced Dagny. :)

What I ended up doing to remove a lot of the shadow striping was set this in skyrimprefs.ini: fShadowBiasScale=1.0000