Seems that the shipping and free form logic were both reset to defaults somehow. I fixed the free form, now I am having issues with the shipping. Nothing is tallying up with shipping. HEre is the segment out of teh user_lib.pl file
$sc_custom_shipping_logic = qq`\@sc_shipping_logic = (
\\\"1DAY|-9.99|||17.00\\\",
\\\"1DAY|10.00-19.99|||18.00\\\",
\\\"1DAY|20.00-29.99|||19.00\\\",
\\\"1DAY|30.00-39.99|||20.00\\\",
\\\"1DAY|40.00-49.99|||21.00\\\",
\\\"1DAY|50.00-74.99|||28.00\\\",
\\\"1DAY|75.00-|||35.00\\\",
\\\"2DAY|-74.99|||12.50\\\",
\\\"2DAY|75.00-|||19.00\\\",
\\\"5DAY|-9.99|||5.00\\\",
\\\"5DAY|10.00-74.99|||8.50\\\",
\\\"5DAY|75.00-|||10.00\\\");
\\\$shipping_price = \\\&calculate_shipping(\\\$temp_total,
\\\$total_quantity, \\\$total_measured_quantity);
\$shipping_price = \&calculate_shipping(\$temp_total,
\$total_quantity, \$total_measured_quantity);`;