You have all been through a lot! Hope you find things improving rapidly in the future.
To double check, the DVT was in the left leg?? The right has developed problems since the incident with brother and falling off bike occurred? And that has to do with pain, rather than weakness? And there is no issue with pain in the right calf or possible new DVT there?
If that is all so, then it is very possible the problems really are a result of the two incidents and not some result of the DVT and hemorrhage. One good things is on the whole, kids tend to be very resilient and heal very well compared with older people.
The problem with x-rays when it comes to feet and micro fractures, is that those small fractures usually don't show up on x-ray. A bone scan can be more successful in this matter. Hopefully you do get to the physio soon. Because you're right, it may be metatarsalgia, however, it could also be microfracturing, or a number of other issues.
You're on the right track with having your son keep active and moving. Have him do so within pain tolerance. So not pushing pain. Check in with the doc again to let him/her know that the foot is still and issue. The doctor may pursue further testing.