The OP doesn't describe the scenario(s) where he/she's having problems - for example - bright conditions or low-light, close-up or distant subjects, all of the above, or none of the above etc etc.
I'm curious what types of shots are being attempted when the issue occurs.
I agree with others, AMFA can make a huge difference in getting the camera to lock focus more quickly and hunt much less.
A free (and arguably less consistent method than some more expensive ones) method is dot-tune... try it on the 35L and see if makes a difference before scrapping the whole works or running out (or mouse-clicking) and buying software and focus targets etc. At least you'll know if AMFA will help, then decide if the FOCAL license is worth the money.
Another simple test is to take a high contrast subject like a chess board for example, align it perpendicular to the camera lens-axis, then place a soup can with a ruler at about 30-45-ish degrees out of plane with the chess board. (basically a very crude lens-align) and just shoot a few shots from about 25x the focal length distance to see if you can tell if it is front or back focusing. That will tell you right away if you need to micro adjust your body/lens combo. (25x focal length example... 35mm x 25 = 875mm or roughly 3 feet at a minimum... for this short distance, maybe use 50x so about 6 feet)... whatever distance you choose, keep it consistent throughout the testing process, DO NOT MOVE the camera.
The AMFA settings are COMPLETELY reversible so don't worry about messing anything up.
Just my two cents based on AMFA'ing my series of lenses on my 6D. Every lens had some level of adjustment needed... some very little, others a suprising amount. Based on my day-to-day use of the camera, AMFA has made a difference and helped me justify buying FOCAL.