There probably isn't a direct link between the Rocky Mountain Spotted Fever and your new knee pain. A doctor would need to tell you for sure. Sometimes there is a residual arthritis that crops up after RMSF or Lyme disease. Both conditions are infectious diseases spread by the bite of a tick.
There are two other possible factors. One is weight loss. If you lost a major portion of body weight during your illness, you may have lost muscle bulk and strength as well. Bones are at increased risk of fracture without the protection of strong muscles around the joints.
The second is your training schedule. Many athletes jump right back into training where they left off instead of building up gradually. Many stress injuries occur when training frequency and intensity are too much too soon.
See a medical doctor before continuing your training program. If you're cleared to go ahead, then step back a few notches and build up your strength first then endurance for the triathlon. If you were off for three months, you can expect it to take three months to regain your former training level.