when u are using silicone please use fairy washing up liquid with water, dip ur finger in it and smooth ur silicone with it....IT STOPS IT STICKING TO EVERYTHING!
And if u want a neat job dip ur finger and use the nail of ur thumb to give a regulated thickness throughout.
u can use bal blue star or any waterproof adhesive they are the best surfaces to tile so long as they are solid, if there are tiles loose remove them and fill the holes with any crappy tiles or something similiar.
in regards to tiling on top of mdf it is not reccomended and this is because the wood drys out the adhesive stopping it to stick properly and eventually coming loose. if it is only a small area i tend to go extreme and use no-nails or an expensive adhesive such as bal-flex. always use ply where...
i think u definately have porcelain tiles and would suggest spending a little cash on a tiling tool we call the holeboy, it is like a g-clamp and is the dogs!!! for holes.
if you have sealed ur tiles with impregnating sealer u should be able to wipe them down with a damp cloth, leave it to dry and then polish with a dry cloth unless u used a ready made grout in which case you will have to wash them several times to remove the film.
you will not to reseal them...