OK. Here it is.
The final output.txt is the exact copy of your example.txt - so said WinMerge (which was used for precise comparison)
All this could be done more compact but I left it as is for better readability and understanding
I included some comments, feel free to ask if you need more detailed explanations about the expressions
Have fun
;FileDelete(@ScriptDir & '\output.txt')
$a = FileRead(@ScriptDir & '\ahihi.txt')
;$a = FileRead(@ScriptDir & '\New For Process.txt')
; insert a newline before $00, $T etc if they are not preceded by colon
$a = StringRegExpReplace($a, '(?<!^|:)(?=\$(?:00|01|03|10|20|25|30|40|45|110|115|120|T|F|200|220))', @crlf)
; delete all content behind $00: and \$200:
$a = StringRegExpReplace($a, '(?<=\$00:|\$200:).+', "")
; delete whole lines $01, $03, $30 including newlines
$a = StringRegExpReplace($a, '\$(?|01|03|30):.+\R', "")
; delete $=<$=T3*1 $=L01836000613000341*000341 and $=L01836000613000341*000341 things
$a = StringRegExpReplace($a, '(\$=<\$=T3\*\d\s*)?(\$=L\d+\*\d+)?', "")
; delete $=P1298*NNNN and \$=>
$a = StringRegExpReplace($a, '(\$=P\d+\*\d+)|(\$=>)', "")
; delete footnotes, not including n1 etc or next $x
$a = StringRegExpReplace($a, '(\$%\$\?\$%[^\$]+Footnotes[^\$]+)(?=n\d+)?', "")
; insert a newline before $%$?$%, some $T and $M
$a = StringRegExpReplace($a, '((?<!^|:)(?=\$%\$\?\$%))|((?<=[a-z]:)(?=\$[TM]))', @crlf)
; move $=S from end of line to start of next line
$a = StringRegExpReplace($a, '(\$=S)(\R)', "$2$1")
; OPTIONALS
; replace unwanted newlines in text parts by a horizontal space
$a = StringRegExpReplace($a, '(\$T|\$%\$\?\$%)\V+?\K(?<=\w|\.)\R(?=\h?\w)', " ")
; replace multi horizontal spaces by only one
$a = StringRegExpReplace($a, '\h+', " ")
; remove horizontal space between $I and $U
$a = StringRegExpReplace($a, '(?<=\$I)\h+(?=\$U)', "")
FileWrite("output.txt", $a)