Hi General Specific, welcome to the board!
I am sorry you have Lyme, but it is good you recognized what it was. Below is a Lyme symptom list. You can have any combination of symptoms.
Unexplained fevers, sweats, chills, or flushing
Unexplained weight change--loss or gain
Fatigue, tiredness, poor stamina
Unexplained hair loss
Testicular pain/pelvic pain
Unexplained menstrual irregularity
Unexplained milk production: breast pain
Irritable bladder or bladder dysfunction
Sexual dysfunction or loss of libido
Change in bowel function-constipation, diarrhea
Chest pain or rib soreness
Shortness of breath, cough
Heart palpitations, pulse skips, heart block
Any history of a heart murmur or valve prolapse?
Joint pain or swelling
Stiffness of the joints, neck, or back
Muscle pain or cramps
Twitching of the face or other muscles
Neck creeks and cracks, neck stiffness, neck pain
Tingling, numbness, burning or stabbing sensations, shooting pains
Facial paralysis (Bell's Palsy)
Eyes/Vision: double, blurry, increased floaters, light sensitivity
Ears/Hearing: buzzing, ringing, ear pain, sound sensitivity
lncreased motion sickness, vertigo, poor balance
Confusion, difficulty in thinking
Difficulty with concentration, reading
Forgetfulness, poor short term memory
Disorientation: getting lost, going to wrong places
Difficulty with speech or writing
Mood swings, irritability, depression
Disturbed sleep-too much, too little, early awakening
Exaggerated symptoms or worse hangover from alcohol
It is very important to see a knowledgeable doctor. Many doctors do not understand Lyme and treat with outdated protocols. Besides Lyme, ticks can also transmit several co-infections including Babesiosis, two types of Ehrlichiosis (HME & HGE), Bartonella, and Mycoplasma. Many people who have Lyme are co-infected. It may affect treatment choice and progress. It is important to be tested for these by a Lyme reputable lab such as IgeneX in Palo Alto, CA. Have you been tested for these yet?
200 mg of Doxy daily is not strong enough for Lyme. I believe the recommended amount is 300-600 mg daily with 400 mg daily often prescribed. There are some important tips about taking Doxy. Do not have any dairy, magnesium, or iron products within two hours of taking it or it will not be absorbed properly. If it makes you nauseous, eat something substantial and non-dairy before taking it. Avoid the sun. You can get a severe burn in minutes even when wearing sunscreen. Do not lay down for at least an hour after taking it, or you can ulcerate your esophagus. This is very painful. Drink a full glass of water when you take it for the same reason.
You are right, early infections are the easiest to cure. Getting the proper treatment now may reduce the chance of long-term complications. You should be treated past the point of where you are symptom free. Is your girlfriend being treated by a knowledgeable doctor? If you need a doctor recommendation, you can email me at firstname.lastname@example.org
Regarding flare-ups, it is important that you get the proper treatment and that you are treated long enough. Often, people are not treated aggressively enough or long enough initially and this can lead to a chronic infection. From what I understand, an infection caught within two weeks of the bite should be treated with a minimum of six weeks of the proper dose antibiotic. If symptoms are still present, further treatment is warranted. A longer infection needs longer treatment. With longer-term Lyme disease, most Lyme doctors will treat until the person is symptom free plus at least two months longer. If co-infections are present, symptoms of each infection can be more severe.
The Jarisch-Herxheimer Reaction (herx) occurs when someone who have Lyme takes antibiotics and their symptoms get worse. When the antibiotics kill the bacteria, toxins are released making them feel worse. It can be scary, but it is a good sign the antibiotics are working. Although it can vary individually, many people experience this at the beginning or change of treatment and every three to four weeks. During treatment it is important to document your symptoms daily. One way to do this is to list the main symptoms you have each day with a numerical rating of their severity from 1-10. Over time when you review this, you can see when your herxes occur and how you are responding to the meds.
Do everything you can to strengthen your immune system--eat healthy, drink a lot of water, exercise whenever possible, do things to detox, get enough rest, take appropriate supplements etc. Whenever you are on antibiotics, it is important to take high-quality acidophilus to replace the good bacteria and prevent yeast overgrowth. The best ones to get are refrigerated and have a high culture count. Most health food stores have them. Wait at least two hours after taking the antibiotic to take the acidophilus.
It is also important to learn as much as possible. I recommend reading Dr. Joseph Burrascano's 2008 Diagnostic Hints and Treatment Guidelines For Lyme and Other Tick Borne Illnesses at http://www.ilads.org/lyme_disease/B_guidelines_12_17_08.pdf He is one of the top Lyme doctors in the country, and many Lyme doctors follow his protocols. He discusses antibiotics and doses starting on page 18. I also recommend the books "Everything You Need To Know about Lyme Disease Second Edition" by Karen Vanderhoof-Forschner and "The Lyme Disease Solution" by Kenneth B. Singleton M.D.
Good luck with your treatment.