The method 999.03 for measurement of fructan were designed to measure just inulin and branched-type (agave) fructans but did not give the complete hydrolysis of levan. 

The 2018.07 method is measuring of all types of fructan (inulin, levan, and branched) in a variety of animal feeds and pet foods. The method principle is exactly the same as in the previous method, however in the new method there is another enzyme involved allowing levan hydrolysis. 
The method you would be following is 2018.07, however if your sample does not contain any levan type fructan the values are going to be the same as when analysed by AOAC Method 999.03.

Limit of Detection of the kit is 1 g/100 g so you would be at lower limit of detection with your samples.

Also incubation with the sucrase enzyme has changed to 30˚C (rather than 40˚C), and is more stable in the presence of BSA, which is added to the buffer.

We recommend to watch the presentation which is very informative: Measurement of Fructan in Biological Materials Presentation