Squirrel had soft poo issues on and off for quite awhile the first several months. I did chicken and rice just like vivienne00 stated (I still do this and I eat half!); I did smaller portions like alan j. mentioned, which would help some, did the yogurt trick at night and even started giving the probiotics every morning as recommended by the Great Dane Lady when switching food and by LindaH. All worked for short time, some foods worked well, others, no matter how expensive, came out faster then she inhaled it.
What was finally figured out by a super nice lady at a little pet shop in Mt Pleasant, SC was that Squirrel needed food with at least 6% fiber...simple as that. I had such tunnel vision on how much protein/fat/calcium/phos/etc that fiber never crossed my mind.
She is on her 3rd bag of Pure Vita grain free (Bison right now) and gets raw when I have it, along with raw frozen fish for treats and hasn't had any issues in a long time.
Just a thought that might be worth looking at for your pup!