You will need the pedal box off a valver and fab it into the car.
Late 8v had the brackets ready to go, what year is it?
You don't need hydro unless you are going for power, which would be an engine and box change anyway.
I'd save the money until then.
Patches on the sills is only a temp fix imo, also budget for some floor/inner sill work to join the new outer sill section.
Sun roof can be a real pita, check the drains first a search on here will throw up loads of information.
Rust is your main enemy, it's been sitting and you know about the sills.
I'm betting you have a few bungs rotted out and others, so check thoroughly before you take on Mk3 
Every thing else is easy and cheap.
TBH, if the vehicle stays with me for a year or so, then it will be going big power, circa 650hp from a Valver should be interesting. We build plenty of fast cars so want to build one for myself again (previous being 430hp Focus RS Mk1 with C63 AMG brakes, and before that a 520hp Zetec Turbo Escort RS Turbo S2)
Ill just get it running right for now and use it as my work horse until I decide what to do with it.
This is a VERY early model - 92 or 93 (J plate)…so I doubt it will have the necessary brackets in place for a hydro conversion. Out of curiosity, what work is involved? Welding brackets etc in to?
Inner sills appear to be fine, but time will tell when I peel the kit back to see whats lurking underneath.
Thing is, for the price I'm going to pay (less than £100), its worth the gamble! If it doesn't work out, I can make the money back just by scrapping the car!
Ill search for the sunroof leak problem, I'm hoping its just a seal or something…if its something major, might just make the perfect excuse to cut the roof off and go for a carbon roof instead!
Thank you all for the great input so far! I will hopefully be going to see it tomorrow again and hope to get it moving!