When trying to decipher what the aphasic patient meant by the phrase "tackle the bear", Foreman asks him if he meant 'bear' or 'bare'. This does not make sense because, as Foreman himself explained earlier, the patient's jumbled words sound completely normal to himself. So in his mind, he said neither 'bear' nor 'bare' but something completely different, and not even he himself can know which word his impaired brain used to replace the one he actually meant to say.
At the end Foreman looks at the blood smear which shows a motile parasite and says it's malaria. Malaria isn't caused by a motile parasite. The parasite shown looks like treponema pallidum which causes syphilis.
The organism seen microscopically near the end was plasmodium falciparum which is a protozoan parasite seen in blood with stains. The image seen was likely a classic darkfield microscopic view of t. palladium.
House and Stacy travel by air from Princeton NJ to Baltimore MD. That distance can be driven in about two hours, so it's unlikely that they would fly. The air travel is likely just a plot device so that they can be stranded overnight by bad weather.