If you had had a tooth which was extracted before, or any infection or unsterilized part, the implant may fall. Things such as smoking, insufficent bone density, a surgery in unsterilized area, loading the teeth right after the implant surgery and no osseointegration period, and medical conditions can cause this problem.
There is surely a risk of damaging the Zirconium crown, but it is still possible to make the root canal treatment without any problem. It can only be decided and seen during the treatment process.
The dental crowns can be bigger than thought if the teeth cannot be or are not shaved down enough. The solution could be removing the crowns, shaving the teeth as much as needed, and then having smaller crowns instead.
The reason you had IPR is most likely to create enough space to fix the open biting. You may want to have veneers to change the appearence of your teeth, however, you will need to have them shaved down for this treatment. The decision is yours whether it's worth it or not.
The gum will fill the gaps when it is healed properly if the veneers are made anytime soon. Please be patient and allow your gums to recover, and then you will see the problem is solved.