Hi and WELCOME to YT
! Congrats on your new baby! And bless your heart for rescuing him and taking such good care of his health...it sounds like he really needed some major TLC.
As far as how to get him back on track...my biggest concern is that he had giardia; these wreaks havoc on the small intestine, most especially in puppies, they're very vulnerable to longer-term effects due to giardia (mushy poos, grainy poos, mucus etc). If I were you, I'd give a probiotic for a good 6mths at least - I like the one from Natures Farmacy:
DOGZYMES® Probiotic Max – 1 Pound » Natures Farmacy Inc.
Would love to see a pic of your kiddo!