Here is a quick stab at your question based on what I remember us doing at my last job:
The first thing I would do is put together a product/allergen matrix showing what products have what allergens.
I would try to make an allergen run order next. This identifies what products can be run back to back and what products have an allergen mismatch where alergen specific cleaning must occur.
Then when you have that complete I would create create an allergen cleaning program. Products that have the same allergen may not need a full clean / swab between them just a quick clean of the machine to remove rood residue. Switching from one allergen to a different allergen would require a full clean / swab test to verify that there is no protien left on the equipment.
Also do you have an alergen brush color / cleaning system in place? Make sure the operators are cleaning the brushes after use to prevent cross contamination with them.
You can have a colored label for recieving personnel to put on any alergenic inventory so that it's clearly marked as an allergen on the outside of the pallet.
No storing of one allergen above a different allergen in a racking system. There is a possibility to have the upper one contaminate the lower one with its allergen.
Checking allergen routes to make sure your not moving one allergen through an area that doesn't have it and creating a possible cross contamination event there.
Train your operators on the entire system.
I think that's about it. I'd have to look over the SQF code to see if I missed anything big... it's not in front of me right now.
As for having to change over quickly. Don't cut short your cleaning / verification procedures to speed up the process. If there is one thing you don't want to do wrong it's allergens. Make sure you give your operators the proper amount of time to clean the line down well and the quality lab, or whomever maybe testing the line, the time to swab it or verify the absense of alergenic protien properly.
You can put advisory statements like that on your products but what your really going to do is drive customers away. If you create a solid allergen system, validate its effectiveness, verify the policies and procedures, etc. you'd be better served without it.