Is the soundproofing stuck to the floor? Its up to you but i know i would remove and sling it, dosent make that much difference noisewise IMO and if its soaked you'll be amazed how heavy it is with all that water in it

Not sure how your drain channels are but on my RS1600i theres two little holes in the opposite corners at the front which drain down into my sills i think

Get a small watering can, open the sunroof and carefully pour a little water into the recess and see if it drains away. If theyre blocked you can try cleaning them out with a small rod (i used the old rails off a hornby train set, curved ones are the best )

have you tried Hadrian www.carpanels.co.uk for the floor panels? you could cut them out another vehicle if you can find one with zero rust

Does the RS2000 have a vin number stamped in the floor?