That is not an out of the ordinary complaint about SQF. SQF is known for telling you what to do but having absolutely no direction on how to do it. The fact is they don't care how you do it so long as you do all of the provisions they direct... If that makes sense.
One very important thing that may help you is asking if you or someone else at your location is an SQF certified SQF Practitioner. The SQF practitioner course is a two day class that helps explain everything needed to certify a location with SQF. Some people have taken it, like me, and say it helped. Some people don't take it and still pass. Personally I like to soak my jobs for as much training as I can get
In Module 2 all you need to really pay attention to is the far right side that is the SQF level 3 column... though it will have everything from the other 2 columns (SQF Level 1 and 2) within it.
The biggest difference you will find, I believe, between FSSC and SQF Level 3 is that you have to have a food quality plan with food quality controls that are just like your food safety plan. You will fail if you consistently send out product that are outside your food quality parameters because SQF Level 3 elevates food quality to the same level as food safety.
In the later modules you have to select the proper ones for your industry. You will find that list in section 1.2 on page 28 and 29. SQF Food Sector # 22 is Processing of Cereal Grains and Nuts which I suspect is your food sector. You will see to the right of that you need to conform to modules 2 and 11 (2 I told you about before) so you can flip down to module 11 which is going to be more of the prerequisite program side of the standard.
It's really not too hard to work with when your accustomed to it.
In case you haven't heard SQF is also now doing unannounced audits one audit out of 3 in an audit cycle. So say your audit cycle is 2015,2016,2017 then one of those audits will be unannounced. (I'm 98% sure I'm right on this... I work in FSSC now but I was paying attention when this came out because I'm waiting for FSSC to come out with this)
My suggestion is to download the module 2 and 11 guidance document that will explain to you what you need to show to satisfy the code and get a gap analysis file (which may be outdated because SQF 7.2 is coming out this year) and just figure out where you are against the SQF code then look at what remains and we can help you with the rest.
I hope my long and poorly constructed explanation helps you some.