Ruling on combining prayers in a marketplace due to heavy rain, knowing that some people performing prayers are customers?

Is it permissible to make up missed prayers at the times in which praying is disliked?

All perfect praise be to Allah,The Lord of The Worlds                                                                                                                                                                        It is permissible to make up missed prayers at any time even that in which praying is disliked. Absolute supererogatory prayer is forbidden to be performed at the times in which praying is disliked, and this also applies to Ihram and Istikhara prayers. However, there is no harm in offering prayers in Mekah during those times. And Allah Knows Best.

What should a praying person who doubts having offered one, or two prostrations in the third Rakah (unit of prayer) do?

Whoever has doubts about their prayer should consider what is less i.e. the above person should offer another Sajda (prostration) and complete his/her prayer, then offer Sujood As-Sahw (prostration of forgetfulness). And Allah Knows Best.

Is it permissible to go to the bathroom wearing a necklace that has the word "Allah" inscribed on it?

All Perfect Praie be to Allah, The Lord of The Worlds, and may His Peace and Blessings be upon our Prophet Muhammad and upon all of his family and companions.

Anything that contains words pertaining to Allah, The Almighty, is desired to be left outside when going to the bathroom, or to be hidden for fear of losing it. And Allah Knows Best.