Concatenating rows in CSV files and removing old CSV files
Clear

List Comprehension

It's an unneeded habit in Python to pre-declare your variables.  Instead of 

myList = []
for x in otherList:
    myList.append(foo(x))


you can use list comprehension,

myList = [foo(x) for x in otherList]
# identical: myList = map(foo, otherList)


Clarity


for f in files:
    file_ints.append(int(f[:8])) #converts file names to ints from datenumber



The comment explains that f[:8] returns the date number of the file but how that happens is a mystery to me.  Why don't you just use os.path.getctime?

file_ints = [os.path.getctime(f) for f in files]


This next bit is confusing.


# makes a valid file path from of the lowest value datenumber
del_file = raw_dir + str(min(file_ints)) + '.csv' 



If only makes sense if your files' naming convention is based on their ctime.  You aren't defining that naming convention here.  Don't rely on external rules. Your file_ints line up with your file_paths so just use

del_file = file_paths(min(file_ints))


You might consider maintaining the alignment by zipping the two together like this

path_mtime = zip(file_paths, file_ints)


Assumptions

Do you get the files daily?  Is the script guaranteed to be run daily?  If both of these are ever false then your clearing will be out of sync.  You are not deleting every file older than 14 days, you are deleting the oldest file if there are more than 14.  It could be 15 days old, it could be 3 day's old.

Instead, iterate over all files and delete anything older than 14 days.

for path, ctime in zip(file_paths, file_ints):
    if is_too_old(ctime): # implement externally.  use time module to get today.
       os.remove(path)


You are also assuming all files in this directory are .csv.  I don't know the nature of the directory but it could be possible that some jerk comes and drops a .txt or .xls in your directory.  os.listDir will also return any subfolders that you might have.  You might not have them but if you did you surely don't want to remove them. Using glob might be the safer bet.  It will also return the full path so you don't need the intermediate files variable.

file_paths = glob.glob(os.path.join(raw_dir, "*.csv"))


This is optional though. It might be more than fair to assume what is or isn't in your folder.

Results

import glob

def clear(raw_dir):
    """ remove any raw csv files that are older than 14 business days. Data itself
    is not lost because it has been archived in the full csv"""
    file_paths = glob.glob(os.path.join(raw_dir, "*.csv"))
    # Optional early exit assuming you get no less than 14 files a day.
    # if len(file_paths ) &lt;= 14:
    #     return
    file_ints = [os.path.getctime(f) for f in file_paths]
    for path, ctime in zip(file_paths, file_ints):
        if is_too_old(ctime): # implement externally.  Use time module to get today.
           os.remove(path)
           print path + ' was deleted in clean up'


Merge

You declare this variable, and then never use it,


archive_file = archive_dir + date + '.csv'



the same value is used at the end,


shutil.copyfile(today_dir + 'TODAY.CSV', archive_dir + date + '.csv')



but I say drop the declaration and leave the end as is, except please use os.path.join

Order

The main issue with this procedure is the order you perform events.  Currently, it is


open output file
read input files
write output file.


It should be,


read input files
open output file
write output file.


reading before you create the output file will simplify the read to,

rows = []
files = os.listdir(raw_dir)
for fi in files:
    if fnmatch.fnmatch(fi, '*.csv'):
         rows.append(open(os.path.join(raw_dir, fi)).readlines())


using glob will make it simpler,

rows = \
    [open(fi).readlines() for fi in glob.glob(os.path.join(raw_dir, "*.csv")]


Clarity

I have no idea why you are transposing your rows.


iter = izip_longest(*rows)



Each row is the list of lines of a file so 

rows = [[line1_file1, line2_file1, ...], [line1_file2, line2_file2, ...], ...]


then you transpose that, so you get 

iter = [[line1_file1, line1_file2, ...], [line2_file1, line2_file2, ...]]


So then each line of your output is a join of the non-null lines of your files.
Are you sure that's what you want?  I could help you more but I don't understand the process you are going through.  Your output file looks like it could be


line1_file1 line1_file2 line1_file3
line2_file1 line2_file2 line2_file3
line3_file1 line3_file3
line4_file3



Point is it's confusing and there should be some explanation.

Results

def merge(raw_dir, today_dir, archive_dir, date):
    """Read through all .CSVs in RAW directory and merge rows into Today's "full" CSV
    """
    rows = \
        [open(fi).readlines() for fi in glob.glob(os.path.join(raw_dir, "*.csv")]
    merged_file = os.path.join(today_dir, 'TODAY.CSV')
    archive_file = os.path.join(archive_dir, date + '.csv')
    with open(merged_file, 'w') as f_obj:
        # whatever is going on here...
        for row in izip_longest(*rows):
            f_obj.write('   '.join([field.strip() for field in row if field is not None]) + '\n')
        shutil.copyfile(merged_file, archive_file)