Thresholds are easy to remove and raise.
For the toilet flange, what I ended up doing was
cutting ceramic tile in the shape slightly smaller than the base of the
attaching it with silicone caulk to the base of the toilet. Not the
best but it works. Only downside is it is hard to get an attractive
bead of caulk.
Take a look at this site. They have a great forum for tiling.