The OP experienced problems with using setFormula returning #REF rather than inserting the desired formula.
Modified code is shown below. There are several areas of change, and escape of characters is the major point. I am NOT and do NOT claim to be an expert in the rules for escaping of characters, I have simply found through trial and error the following to be necessary for this code to be successful.
- when a formula refers to a sheet name, it's not necessary to have single quotes around a sheetname unless there is a space in the name.
 
- when a formula includes a sheet name containing a space, then the sheetname should be surrounded by single quotes however the single quotes should not be escaped.
 
- as a general statement, it's not necessary to escape double quotes unless the object contains spaces or other punctuation characters. For example: 
var c1r1ct (line 48) includes a date definition which contains spaces and commas, a colon and a forward slash. Similarly, var memData1 and var memData2 include an option containing a fullstop (period) as well as spaces. 
IF statements appear to require all double quotes to be escaped; probably because the formula includes a variety of punctuation types. 
Note: to escape a character insert a backslash
There were also several changes unrelated to formatting, but rather the formula was directed at the wrong cell.    
var c1r1tz = setup.getRange("C4") & var c1r2tz = setup.getRange("C5") should refer to E4 and E5. 
var c1r1ct = setup.getRange("D4") & var c1r2ct = setup.getRange("D4") should refer to H4 and H5 
var c2r1tz = setup.getRange("C12") & var c2r2tz = setup.getRange("C13") should reference E12 and E13 
var c2r1ct = setup.getRange("D12")& var c2r2ct = setup.getRange("D13") should reference H12 and H13 
var c1r1ct, var c1r2ct, var c2r1ct, var c2r2ct, var mrsub1, var mrsub2, var memData1, var memData2 - escape double quotes (only). Because the formula included both single and double quotes. 
var memData1, var memData2 - escape the period (.) in the formula 
function so5461418804() {
  // WAR ROSTER FIXES
  var matchtool = SpreadsheetApp.getActiveSpreadsheet().getSheetByName("Match Tool");
  var setup = SpreadsheetApp.getActiveSpreadsheet().getSheetByName("Set Up");
  // Match Tool Tab Formulas
  // Clear Content
  var clear1 = matchtool.getRange("E8:F57").clearContent();
  var clear2 = matchtool.getRange("L8:M57").clearContent();
  // Reformat Alignments for Clan 1
  var c1center1 = matchtool.getRange("A:A").setHorizontalAlignment("center"); //Left Numbers
  var c1center2 = matchtool.getRange("B7:B").setHorizontalAlignment("center"); //MR Sub Column
  var c1center3 = matchtool.getRange("D7:E7").setHorizontalAlignment("center"); //Player ID, Name
  var c1center4 = matchtool.getRange("F7:F").setHorizontalAlignment("center"); //TH Column
  var c1left1 = matchtool.getRange("C8:E").setHorizontalAlignment("left"); //Check Mark, Player ID, Name
  // Reformat Alignments for Clan 2
  var c2center1 = matchtool.getRange("N:N").setHorizontalAlignment("center"); //Right Numbers 
  var c2center2 = matchtool.getRange("I7:I").setHorizontalAlignment("center"); //MR Sub Column
  var c2center3 = matchtool.getRange("K7:L7").setHorizontalAlignment("center"); //Player ID, Name
  var c2center4 = matchtool.getRange("M7:M").setHorizontalAlignment("center"); //TH Column 
  var c2left1 = matchtool.getRange("J8:L").setHorizontalAlignment("left");
  // MR or Sub Formula
  var mrsub1 = matchtool.getRange("B8:B57").clearContent().setFormula("=if(or(D8=\"\",D8=\"Player Not Found\"),\"\",if(iferror(Match(D8,'MR1'!$B$6:$B$67,0)),\"MR\",\"Sub!\"))");
  var mrsub2 = matchtool.getRange("I8:I57").clearContent().setFormula("=if(or(K8=\"\",K8=\"Player Not Found\"),\"\",if(iferror(Match(K8,'MR2'!$B$6:$B$67,0)),\"MR\",\"Sub!\"))");
  // Roster Member Data Formula
  var memData1 = matchtool.getRange("D8:D57").clearContent().setFormula("=if(or(C8=\"\",C8=\"\.     Blank\"),\"\",iferror(index('MR1'!$B$8:$D$87,(match(C8,'MR1'!$J$8:$J$87,0))),\"Player Not Found\"))");
  var memData2 = matchtool.getRange("K8:K57").clearContent().setFormula("=if(or(J8=\"\",J8=\"\.     Blank\"),\"\",iferror(index('MR2'!$B$8:$D$87,(match(J8,'MR2'!$J$8:$J$87,0))),\"Player Not Found\"))");
  //Set Up Tab Formuals
  var acctsleft = setup.getRange("C24").setFormula("=if(not(isblank(D19)),C19-SUM(C20:C23),\"\")"); //Account left in Break Down
  var abbr = setup.getRange("F21").setFormula("=if(D1=\"Grand Warden League\",\"GWL\",if(D1=\"Archer Queen League\",\"AQL\",if(D1=\"Barbarian King League\",\"BKL\",if(D1=\"Battle Machine League\",\"BML\",if(D1=\"Clan Castle League\",\"CCL\",\"\")))))"); //Set's the League Abbrivation for a shorter Standard Breakdown formula
  var stdBD12 = setup.getRange("D20").setFormula("=if(F21=\"GWL\",5,if(F21=\"AQL\",3,if(F21=\"BKL\",2,if(F21=\"BML\",1,\"\"))))"); //Sets the Standard Breakdown for TH12s
  var stdBD11 = setup.getRange("D21").setFormula("=if(F21=\"GWL\",12,if(F21=\"AQL\",8,if(F21=\"BKL\",5,if(F21=\"BML\",3,\"\"))))"); //Sets the Standard Breakdown for Th11s
  var stdBD10 = setup.getRange("D22").setFormula("=if(F21=\"GWL\",18,if(F21=\"AQL\",19,if(F21=\"BKL\",13,if(F21=\"BML\",8,\"\"))))"); //Sets the Standard Breakdown for TH10s
  var stdBD9 = setup.getRange("D23").setFormula("=if(F21=\"GWL\",0,if(F21=\"AQL\",0,if(F21=\"BKL\",5,if(F21=\"BML\",8,\"\"))))"); //Sets the Standard Break Down for TH9s
  //Clan 1
  var c1id = setup.getRange("J2").setFormula("=index(MRTool!B1:B39,Match(D2,MRTool!A1:A39,0))"); //Clan 1 ID#
  var c1r1n = setup.getRange("B4").setFormula("=index(MRTool!$D$3:$D$53,match(D2,MRTool!$A$3:$A$53,0))"); //Rep 1 Name
  var c1r2n = setup.getRange("B5").setFormula("=index(MRTool!$F$3:$F$53,match(D2,MRTool!$A$3:$A$53,0))"); //Rep 2 Name
  var c1r1tz = setup.getRange("E4").setFormula("=index(MRTool!$E$3:$E$53,match(D2,MRTool!$A$3:$A$53,0))"); //Rep 1 Time Zone
  var c1r2tz = setup.getRange("E5").setFormula("=index(MRTool!$G$3:$G$53,match(D2,MRTool!$A$3:$A$53,0))"); //Rep 2 Time Zone
  var c1r1ct = setup.getRange("H4").setFormula("=if(E4=\"\",\"\", TEXT('TZ Table'!$I$1+index('TZ Table'!H:H,match(E4,'TZ Table'!B:B,0))*time(ABS(index('TZ Table'!E:E,match(E4,'TZ Table'!B:B,0))),index('TZ Table'!G:G,match(E4,'TZ Table'!B:B,0)),0),\"dddd, mmm dd, h:mm AM/PM\"))"); //Rep 1 Current Time
  var c1r2ct = setup.getRange("H5").setFormula("=if(E5=\"\",\"\", TEXT('TZ Table'!$I$1+index('TZ Table'!H:H,match(E5,'TZ Table'!B:B,0))*time(ABS(index('TZ Table'!E:E,match(E5,'TZ Table'!B:B,0))),index('TZ Table'!G:G,match(E5,'TZ Table'!B:B,0)),0),\"dddd, mmm dd, h:mm AM/PM\"))"); //Rep 2 Current Time
  //Clan 2
  var c2id = setup.getRange("J10").setFormula("=index(MRTool!B1:B39,Match(D10,MRTool!A1:A39,0))"); //Clan 2 ID#
  var c2r1n = setup.getRange("B12").setFormula("=index(MRTool!$D$3:$D$53,match(D10,MRTool!$A$3:$A$53,0))"); //Rep 1 Name
  var c2r2n = setup.getRange("B13").setFormula("=index(MRTool!$F$3:$F$53,match(D10,MRTool!$A$3:$A$53,0))"); //Rep 2 Name
  var c2r1tz = setup.getRange("E12").setFormula("=index(MRTool!$E$3:$E$53,match(D10,MRTool!$A$3:$A$53,0))"); //Rep 1 Time Zone
  var c2r2tz = setup.getRange("E13").setFormula("=index(MRTool!$G$3:$G$53,match(D10,MRTool!$A$3:$A$53,0))"); //Rep 2 Time Zone
  var c2r1ct = setup.getRange("H12").setFormula("=if(E12=\"\",\"\", TEXT('TZ Table'!$I$1+index('TZ Table'!H:H,match(E12,'TZ Table'!B:B,0))*time(ABS(index('TZ Table'!E:E,match(E12,'TZ Table'!B:B,0))),index('TZ Table'!G:G,match(E12,'TZ Table'!B:B,0)),0),\"dddd, mmm dd, h:mm AM/PM\"))"); //Rep 1 Current Time
  var c2r2ct = setup.getRange("H13").setFormula("=if(E13=\"\",\"\", TEXT('TZ Table'!$I$1+index('TZ Table'!H:H,match(E13,'TZ Table'!B:B,0))*time(ABS(index('TZ Table'!E:E,match(E13,'TZ Table'!B:B,0))),index('TZ Table'!G:G,match(E13,'TZ Table'!B:B,0)),0),\"dddd, mmm dd, h:mm AM/PM\"))"); //Rep 2 Current Time
  var flsuh = SpreadsheetApp.flush()
}