Jennifer, funny I was going to add (but got interrupted and then forgot) that these funny turns don't sound thyroid related and should be checked out - so I'm glad you did. Your symptoms could all be related to the urine infection. After 2-3 days of the antibiotics, you should start to feel better from the urine infection. If any symptoms remain after you finish the antibiotics it'll be easier to work out what is the cause of them. As well as taking antibiotics, drinking lots of water and no sugary drinks, will help resolve the urine infection.
Ok, so back to thyroid. You mentioned you had problems when starting on the 100mcg, it would be interesting to know what these problems were. So we can work out the likely cause(s).
Based on my experience (but no medical qualifications) there are some things I can think of that are relevant. To summarise, you said you were still getting hypothyroid symptoms when taking thyroxine at 100mcg and your blood tests indicated you were under medicated and your doctor advised you to increase your dose. Thoughts here are: make sure you get a printout of your blood test results each time (it sounds like you are already doing this) they're very informative - they usually show the ranges next to your result, so you can check for yourself what's going on. Even when a result is in range, it's worth noting whereabouts it is in the range (bottom, middle, top).
When increasing or decreasing the thyroxine dose, I find it's best to do so slowly by chopping the 25mcg tablet into quarters and increasing/decreasing by a quarter every 2 days. By doing this you will have increased by 25mcg by the end of 8 days. This gives one's body time to adjust and decreases the side effectsYour next question was about becoming pregnant. I would very strongly advise you to get your thyroid stable first. I know a sample size of one isn't valid to draw conclusions from, but I'm going to do so anyway. My thyroid levels were low when I was pregnant with my first child (there is a time lag before the blood test reflects one's thyroid hormone levels). This child has a mental health condition which I'm convinced is because my thyroid hormone levels were too low during pregnancy (I kept detailed records). I think it's only a matter of time before this connection will be demonstrated - there has recently been some research that has shown that children born to mothers who had low thyroid hormones have problems with mental maths and stunted growth (google: daily mail hypothyroid mental maths). Both of which apply to my child. So, please do wait until your thyroid levels are under control.
There are a number of steps in the thyroid process and all of them have to be working optimally for us to feel good. For most people, step 1, supplementing with thyroxine (T4), works well once the correct dose has been determined. For a sizable minority (about 15%) the next step(s) in the process are also faulty. Step 2 is the body converting the T4 to T3 (liothyronine, the 'usable' thyroid hormone). If one's body isn't doing this step properly then one will have hypoactive symptoms, but will get blood test results showing one is over medicated: TSH below range and T4 at top of range. This is because the T4 isn't being converted to T3 and is still in one's blood, giving the high T4 blood test result. It also means one's body doesn't think it needs any more T4 so doesn't supply TSH (thyroid stimulating hormone) and your TSH reading will be low. Thereby implying that you're over medicated despite having hypothyroid symptoms. The reson for mentioning this us, at the moment you don't know whether you are going to have your hypothyroidism managed by merely supplementing with T4, or whether other action is going to be needed. I'm in the group who aren't converting T4 to T3 and have needwd to switch to taking Natural Desiccated Thyroid (NDT) as it contains T3 as well as T4.
I've read somewhere that the body processes thyroxine better at night. This is why you changing to taking it at night may have helped you. For me taking it at night was like getting a kick start and I couldn't sleep. You may find as you get nearer to the right dose that you prefer to take it in the morning.
Yes do give the increased dose time to settle in. You should find the random aches and pains and other hypothyroid symptoms (lack of motivation, inability to focus/concentrate, tiredness etc) decrease. For me, it takes 3 months from a change in dose to be correctly reflected in the blood tests. Others say 6-8 weeks. So you need to get another blood test at about 12 weeks if you feel ok, at 6-8 weeks if you are still getting hypothyroid symptoms.
I've had an underactive thyroid for 25 years and have learnt a lot in that time, so if you have any more questions, just ask.