I'm not sure I'm using correct bolts on mine 289 05/1965 w/4speeds trans. Not sure also if they are zinc or other color.
Did you read the entire thread? If you look in this forum's library under topic "Mustang Hardware Spreadsheets 64-66" you will find two files, one by part number (almost every hardware item on these Mustangs has one) and one by application (aka where it goes). To answer your question, the answer is "yes". Confused? Look under "TRANS,MT (in your case)" for some answers.
Pictures of those bolts show "late American rust and corrosion". Originals were "natural" steel covered in a lite oil, stored in a big container on the assembly line. To reduce future rust on mine, I prefer a dull zinc plating (vs clear zinc). I'll let those in the "rust belt areas" give you their alternatives.
Jim