Various pet rat problems

Question
Two months ago I moved in with my now husband and we together have four female rats. We drove my rats up from Louisiana to Idaho. Mine (Kimmy and Lulu) and his (Cassie and Penny) were living in separate cages. We let them meet and socialize for a few days (they got along great) then we moved them all into the larger cage. We are saving money for a larger, custom-built cage. They use Carefresh bedding, no-ink newspaper endroll paper for nesting, and eat a homemade blend of Storebought lab blocks and Sue-bee's rat mix which contains various grains, Total cereal flakes, dried fruit, soynuts, dried pasta, etc. All was going well until Penny started getting an upper respiratory infection. Around the same time Kimmy started to get various wounds all over her body (back, face, and stomach). We assumed they were fighting over food, so we tried separating Kimmy during feeding. We soon separated Penny (she was losing weight) so she could eat by herself (she was always a tiny rat). We took her to the vet and they gave her two weeks of Baytril and Doxycycline. She is still very thin (though her appetite has increased since she ran through her course of medication). I've been trying to feed her separately, but sometimes she won't eat. Kimmy is by herself in the smaller cage, so her wounds can heal, but it literally seems like she's getting MORE of them. I'm keeping an eye on them so they don't get infected, but the scabs are just reappearing and she is absolutely covered in them. Are these battle wounds (and if so are they fighting because of food or a more crowded cage?) or are they self-inflicted or could they be mite irritations? We are already very tight on money. I never had these problems when I had just Kimmy and Lulu. Lulu only got a small "cold" which she recovered from in a day and a degloved tail tip which was amputated and healed perfectly. These are also my first rats, which I have had since October 2012. My husband has had his rats since January 2013 and they were put in the same cage June 2013. I never have had rats before this so I am fairly inexperienced in all the various problems they may have.

Answer
Hi Emily, first, congratulations on your very first rats.  You say you are not that experienced with rats, but it sound as though you are providing good care, a good home and excellent diet, so that is a very good start!

I am fairly certain that Kimmy's "wounds" are not wounds caused by the other girls from fighting, but are a skin infection, possibly caused by mites, or perhaps excess of protein in her diet.  Please do put Kimmy back into the main cage with the other girls because keeping her by herself is probably causing stress, and in rats, stress hinders healing.

I'm sending you a link to a web page regarding skin infections in rats, written by a very knowledgeable rat expert and a friend of mine.  The information is written in somewhat of a humorous way, but trust me that it is very accurate.  She details what should be done for treatment for this.  
Here is the link -->  http://www.sandyscrittercity.com/skinproblemsabscesses.htm

The other pages on her website are also very informative and would be very useful to you on your road to rat ownership so I highly recommend reading through all of it to learn as much as you can.  http://www.sandyscrittercity.com.  A few other good web sites for rat information include http://www.ratcare.org/  and  http://ratfanclub.org/  

Your vet treated Penny with the correct medications, but for not a long enough period of time.  21 to 30 days is recommended in order to rid the body of the infection entirely and a relapse may occur.  I am glad to hear Penny's appetite is improving, but should you see any signs of relapse of the URI, insist that the vet prescribe a minimum of 21 days of these meds.

I hope that this was helpful and that both your girls recover soon.  Please let me know if I can help you with anything else.  
(By the way, 2 of my current 3 female rats are also named Penny and Lulu...what a coincidence!)