I'm not a TCM practioner, but have used TCM for a few years and Spring Forest for the last 12 months, and have also had 'heat' in the gall bladder and liver myself. I continue to take TCM herbs to clear the heat, and practise SFQ daily.. All the SFQ level 1 exercises will be of help to you, I know that Harmony of the Universe and Seven Steps, (Moving of Yin and Yang is always good too) are particularly beneficial to the Liver system.
From the Level 2 exercises I'm finding 10,000 Hands incredibly beneficial, 10,000 hands works on the Liver, Intestines, and Lungs. If you have the level 2 manual it might be a good idea to try that exercise. Master Lin is doing a series on Liver Energy this month on the Healing Connection (find it on the SFQ site), so maybe you should sign up for the last week and listen in? Next week he will be focusing on the specific Qigong exercises for the Liver. You can also submit questions to Master Lin on the Healing Connection so maybe that's an idea too.
In terms of fatigue, if it's related to weak Kidney energy I've found Master Lin's advice to do the Qigong exercises in a lower stance to be very beneficial. Your legs start shaking and the energy pumps up your legs to your kidneys, and the more you can do the more vitalised you will feel. Try bending your knees a little further when standing up and practicing, when your legs shake just let them, it will likely come in waves. Listen to your body and don't strain yourself at any point though, as to avoid injuring yourself and creating further blockages.
I think with SFQ, the more you can do the better. If you feel stressed/anxious after SFQ practise, it's likely a sign that blockages are clearing. Personally after particular exercises I feel strange sometimes for a few hours after, so I tend to practise those exercises either at night before bed, or when I have few social obligations that day.
I'm sure your TCM doctor has told you this, but do your best to minimise spicy and fried foods, alcohol, caffeine (even chocolate). This will really help your system while it clears the heat from your Liver/Gallbladder.
With herbs, acupuncture and SFQ I'm sure you can make a good recovery! good luck :-)