Several questions and several answers.

• particuller: indeed, as you guessed, it should be particulier. Particulier is here an adjective that emphazises its noun. In English, is it not correct to say “We were particularly careful in removing...“? Here it would be the same idea. And even it is tout particulier as a whole (here tout does not have a meaning of complete). tout emphasizes particulier, which means soin is doubly emphazised (sort of we were really really particularly careful, I swear). It is called marketing ^^.

• Indeed, it is ait. It is subjunctive of avoir. Subjunctive is needed after bien que.

• en is here a pronoun, that means of them. Il peut en rester quelques-unes => Il peut rester quelques-unes [de ces arêtes]. I think your difficulty was that you sought a meaning for pouvoir + en. There is none ! en is not related to pouvoir, here.