Ok so i have finally got to the end of Baptism by fire and im fighting Runt, ive next to no health and no way of getting my health up, how on earth am i to defeat him and when im dead in seconds…
Prepare better 
you should obtain some healing potions before battle, get some poison on your sword, get better armor and stats…
Or as others said… Just shoot him with bow, headshot will end him in no time
I think im way too low of a level to be doing that mission and not enough training
I had the same problem, faced him with 40 % health lol, ended up sheating the sword and popped him a couple of arrows to the head, he went down like a sack of potatoes. Not very chival of me, but got the job done.
Really depends on your preparation and training. In my case, the Runt fight went on like this: perfect shield-block of his first strike, swing around, perfect shield-block of his second strike, and immediately a riposte hitting between his left shoulder and neck (I don’t think it was even a “master strike"). He fell in one strike. It was over so quickly, but was sooo satisfying! 
(Bouche shield, Herod’s sword. I believe he never even touched my armor.)
Given my lack of skill with the combat system I am not going near the main story for a long, long time. Main level 10, Magdeburg & Milanese armour, Magdeburg sword, cutting through bandits like a hot knife through butter, but I would still last about 5 seconds against someone who knows what they are doing.