My son started mepron, and IV zithro, a few weeks ago. He was scheduled for 2 tsp. of mepron per-day, but he couldn't do it. This first course, we're only doing one per-day, but I'm adding 200mg of artemisinin.
The IV doxy was scheduled for 500mg, but he's starting on 250mg per-day. He's herxed on rocephin previously, and he's been herxing on the limited doses of mep and zith as well.
We're going to eventually ramp it up to the correct levels, and we're also pulsing the meds as well.
Many people slowly build up to the desired levels, it's very common.
My husband's LLMD prescribed him 300 mgs/day Doxy. and was told to take 3 times/day during the waking hours (i.e. upon waking, bedtime, and in the middle. For my husband that's 7 am, 3 pm and 11 pm.)
Remember about Doxy -- be upright for at least 30 minutes after taking it -- says so on the prescription information provided by the pharmacy. Has to do with burning a hole in the lining of the esophagus, I think. This happened to someone I know.
Best wishes in your recovery 
p.s. I always took my Doxy about 10 minutes after cookin up and eating a double-serving of hot oatmeal. Anything less made my stomach hurt for several hours after each pill. I hope you can get it down eventually...
Leslie
Also, you might check whether you had the doxy before or after eating. It's so irksome to obsess about this stuff, but you can do better with the doxy if you've eaten and let the food settle a bit, instead of taking the doxy first and letting it be the first thing your stomach sees.
It is VERY hard on your system.If you cannot adjust to the required dosage, there are alternatives to doxy for treating Lyme Disease. Some alternative antibiotics are listed in the following thread: http://flash.lymenet.org/ubb/Forum1/HTML/032580.html
Linda
I can imagine that one can pulse them.
4 days per week 400-600 mg/day and the rest of the week 200 mg/day. It still should work well.