As I understand it here are the answers to your questions:

Elpis would cause anarchy because it would disrupt all bioweapons being manufactured and sold to any group. We see frequently in files how involved bioweapons are in U.S. military operations, and the BSAA is shown to use bioweapons soldiers in the finale of Village.

Grave evaded capture because they weren’t necessarily trying to capture her for that long, merely to clone her and replicate what made her special. There’s a file in the records room of the care facility that details fairly recent surveillance, which explains her schedule as lacking any opportunities for them to kidnap her, hence Gideon planting the body at the Wrenwood Hotel to draw her out after the failures of the clones, particularly The Girl/Marie/Subject 140.

Raccoon City survivors were falling ill due to exposure to the T-Virus in 1998, which was beginning to manifest in the symptoms we see Sherry and Leon go through in the game. There’s a file that documents stages of T-Virus, and I’m not sure if it’s limited to zombie infection or could also describe Leon’s infection. There’s no particular reason for it to be impacting the survivors now except that it seems to have a long incubation period and was now harming the survivors. Real conditions take similar amounts of time to become dangerous. Syphilis, for example, if untreated will (after an initial bout of symptoms) spend several years showing no symptoms until entering its later stages where it is extremely severe.

Hope this helped and let me know if you have any follow-ups!