Most problems with an altered microbiota come from the stomach. So does candida. Chances are that you have low stomach acid/hypochlorhydria.
Doing a test for stomach acidity might be helpful, it's simple and cheap to do but only indicates whether there is a problem. It's not all that accurate. http://www.livingfoods.co.uk/pages/articles/the-acid-test.php
Addressing biofilms requires Quorum Sensing Inhibitors. QSI's stop/interfere with the chemical messages which stops the micro-organisms from signalling to re-enforce the biofilm. That helps a lot because they can re-enforce the biofilm as quickly as it is degraded if they can communicate to do so.
Until I started using QSI's I did not get anywhere but once I started using QSI's I did eliminate the biofilms. However actually defeating the micro-organisms has proven far more difficult.
Suitable QSI's, BFB 1 and BFB 2 are the best known but are not really meant for internal usage. The essential oils contained in those two products can be used internally but pure organic varieties are preferable which those two products do not say they are.
Enzymes such as Interfase/Interfase+. Interfase is best because it contains more enzymes as the plus variety takes up capsule space with EDTA leaving less for enzymes. EDTA is quite cheap and can be put into capsules fairly easily. The only problem is that Interfase+ tends to be cheaper than Interfase circa 1:2.
Dealing with the changes in your microbiota would be better done with a diet designed to promote growth of beneficial bacteria. Diets such as GAPS etc. Just becuase you have had tests which show abnormal levels of bacteria does not necessarily mean the implanted bacteria have changed, it just means that the bacteria going through your digestive system are not ideal. Diets such as GAPS should alter everything in a more favourable way.
Raising the acid forming bacteria in the colon would be helpful.
If you want to do those biofilm protocols which I think are unnecessary IMO then why not eat only quickly digested foods during the day, especially at lunch, avoiding protein and fat. Apples, bananas and carbohydrates. Then do the protocol when you get home.
If you take enzymes close to food, before the stomach is empty, the enzymes will break up the food rather than a biofilm. Your stomach emptying could be slow.
I would say that the only biofilm(s) you need to tackle is the ones in your stomach. You might have a Urease positive infection which neutralizes stomach acid making digestion difficult, you do say malabsorption/maldigestion which could be the result of insufficient stomach acid. Eliminating biofilms in the stomach causes stomach discomfort because the biofilms replace the normal mucosa.