There are various ways to retrieve the text from source PDF document, including the regular expressions and rectangular region of the page. Please refer to these help topics: Extract text from PDF, Extract Paragraph from PDF, and Search and Get Text from Pages of a PDF Document
The checkbox list have child annotations, and we can get or set child annotation with ActiveState property of CheckboxField instance. Please try the code ad follows:
Document doc = new Document("MyDocument.pdf");
CheckboxField cb = doc.Form["chkBox1_04"] as CheckboxField;
//To get/ set value of annotation you can check or fill ActiveState property
//of child annotation or of the field.
cb.ActiveState = "MJ"; //this affects only this annotation, making it checked
cb.ActiveState = "Off";