Have you checked out:http://www.jerry-applegate.org/genealogy/afa/afa-part-1.txt
Then look at:http://www.jerry-applegate.org/genealogy/thomas1/
They are different versions. The second is easier to study, but doesn't have all the names. Don't get overwhelmed. You can use your "Find In Page" function under Edit in Netscape (don't know about IE, but sure there must be something similar). The first time I looked at this page several years ago, I was pretty new to computers and didn't know about this function. It took me all day looking one record at a time, but found my husband's grandfather Frederick Roch Applegate so it was worth it. He is descended through Thomas' son Daniel.
The last time I tried the email address several months ago the mail was returned. But perhaps it is up and running again. Happy hunting. Ellen Applegate