I work for a facility that repacks dried fruits, nuts, legumes, grains and cereals and we are currently SQF level 2 certified.
If I am right, the main allergens in your facility nuts and sulphites (from the dried fruits).
You need to schedule your production so that you start with products that do not contain allergens and end with those that contain the most significant allergens as Tony said.
Secondly you need to clean all the parts of the lines that come in contact with the food product when you do the changeover. In our case we clean the hopper (on the spot) using a disposable tissue with little water, detergent and a sanitiser. The components of the dataweigh that can be dismantled are cleaned in a sink with detergent and a sanitiser. Those that can not be dismantled are cleaned on the spot just like the hopper. When you change from a product that contains one allergen to a product that contains another allergen, the equipment have to be cleaned.The efficiency of the cleaning process could be verified by conducting a swab. There are several swab kits for allergen available. When you changeover from a product that does not contain an allergen to another product you can just flush the lines with high pressure air.
Thirdly, you may also want to have a dust collection system installed with an aspirator on the packaging line.