Can help you with a few of the things you have asked about
The Engine: As far as research goes the original Biohazard games are run off a modified version of the Quake engine and was updated for every other game so RE2 would have probably ran off Quake 2. The way it was modified was to use instead of a FPS perspective was early 3D using pre-rendered backgrounds (I'll get to those in a bit) The only thing Quake would have being rendering is a set of primitive polygon shapes that would act as collision detection so when you moved your character into a wall it wouldn't be able to walk through it. Fire, water Rain in the later games (RE3) would have being created via particle emitters most games engines use these emitters (Unreal, Obviously Quake etc)
The 3D/ Art side: This has being researched to death and pretty much now all the information is out in the open. Capcom used a program called Softimage it was originally created by Microsoft and was the main program 3D artists used for early ps1 games like Final Fantasy VII, Silent Hill the list could go on their just the main ones. Now this tidbit of information was recently found out: Capcom used a set of computers referred to as O2 (Nothing to do with the phone company) these workstations at the time were created to accurately render not only lighting but 3D geometry this is how Capcom modeled their backgrounds/characters. Now apparently each render took 2 weeks to fully render I don't know if this covers entire rooms or just one individual render.
There is also debate as to how the backgrounds match up to the boundaries within the engine one speculation by fans is that they had a custom plugin for softimage that would export not only the renders but also build/ compress a set of low poly primitive shapes similar to Quake into what is known as the .RDT (Room Data) that is found in every Resident Evil Game (1-3) these then would load into quake and as a result you get a room to run around.
REmake and Zero: To make the backgrounds for these games Capcom used Autodesk Maya to model and render the rooms, this is proven 100% by the inclusion of maya's interface in the Resident Evil Archives I book.
Programming wise every game back in that day was coded in C/C++ think now its mainly C# Ps3 games are coded in that.
If you want to know more I would suggest looking for the Resident Evil 1,2,3 modding forums, I can't post links at the moment but if you google search it you should find it there is lots of information about file formats for the old games and even custom built tools that help with modifying the old games (i'm also on there and have a guide to model your own custom backgrounds in maya 2008, and I also post a lot of my custom 3D content)
Anyway hope this all helps.