If your adding insulation between the floor joists it will need to be "faced" (paper on one side, paper side always faces the heated area), then you do not need to add anymore plastic as a moisture barrier on the house side, in fact adding a second layer would be very detrimental to the sub flooring by trapping moisture between the two, plastic should be laid in the craw space to stop ground mositure.
Make sure if your sistering the new floor joists to the existing (what's left of them anyway) that you bolt the joists together, I always use 1/2" bolts and stagger the holes one up, one down, one up...etc...etc.
There is really no need to use pressure treated lumber for the repair, as when fixed there is no more water to worry about, nor is it used in most new builds.
The cutting or notching of the floor joists for the tub drain, isn't all that surprising, it happens much more than you think, in an ideal world the joist should be cut completely and a header added across it from the floor joists on either side of it leaving enough space for plumbing.
Be very careful when using pressure treated lumber under vinyl flooring, many times it can an adverse reaction with the vinyl/glue, also it is very important to make sure it is very dry before adding any sort of covering over the top of it, most pressure treated material is very wet, your best solution would be a product called "Advantech" (Lowe's/Home depot sell it)it is specifically made for flooring and can handle reasonable amounts of water before any noticable failure. It is the most common used flooring product in new quality new builds and the only product I use for new or renovation/repair work.
I always use a bead of construction adhesive on the top of the floor joists before laying the new flooring and I always screw the flooring down, NEVER nail.