@Guilherme has it nailed.
Feet first. If his feet have not been managed properly, he’ll have been compensating in various ways in many parts of his body. As you manage him and get his feet taken care of, you may (very likely, in my experience) see pain “pop up” in places that previously seemed fine, as his body starts to move and load itself more correctly - areas that were overloaded to protect sore heels, for example, may suddenly show their soreness.
Be patient, make sure you feel confident in assessing the work of your hoof care professional - or engage someone you trust who can help you assess. Ensure his diet is feeding his feet properly (eg: my forage provides everything in good quantity AND ratio, except for copper, zinc, sodium, and selenium. There is literally no detectable level of copper in my hay, and it’s critical for hoof health, so I supplement!).
Make sure the horse has the support he needs foot-wise to be comfortable, stimulate hoof health, and to actually use his feet properly. Whether that’s boots, shoes, more turnout, whatever.
If I were in your position, I’d look at this as an opportunity to do a ton of work on the ground and solidify the relationship and his groundwork skills. Then as his feet improve and you get your saddle fitter involved, you’ll be set up for a much better start under saddle.
I take on quite a few creatures who have had rough starts of various categories: rough handling, ignored physical issues, pushed way too quickly, etc. They remember that for the rest of their days - if you have an opportunity to minimize his association of Work = Pain, grab it!