I have a super trick for that, that feels a bit like cheating. Make a rover with all the science stuff you have, and the retractable wheels. When retracted, the vehicle is "not grounded" and you are able to perform "while flying" science.
Your payload is not specially big. Possible causes:
1) Your craft is not symetrical, download the KER mod, because otherwise you can't see your torque (tendency to fall to one size)
2) Control is given to a probe that is not pointing upwards.
3) Boosters are tilty in general, provide a lot of thrust but as weight is reduced it moves the center of gravity. Move (or remove) the boosters down.
4) I have clashing feelings about control surfaces in rockets Sometimes they are a must, others a nuisance. Careful using (so much) of those.