Flying from USA to Frankfurt, Germany then to Prague.

Yes, if your plane is on time.

Will I have to go through customs before boarding the flight to Prague?

Customs is where they make you open your suitcase, etc. and check everything. They don't do this in Frankfurt, neither coming nor going. You will go through passport control, but no one will look in your bag. You have almost 2 hours between landing and departure, which should be plenty if your flight from the US is on time. Which airlines are you using and are they both using the same terminal or will you have to go from terminal 2, to terminal 1?

With changing airlines in Frankfort will my luggage automatically be transferred to the flight to Prague or will I have to go to baggage and pick up my luggage then go to passport control then on to my flight? Sorry for all the questions.

"With changing airlines in Frankfort will my luggage automatically be transferred to the flight to Prague?" It depends. If you're traveling on a single ticket showing Prague as your final destination, your bags will probably be transferred automatically. Ask when you check in, to be sure. If you bought a separate ticket for your Frankfurt to Prague leg, you'll definitely have to retrieve and re-check your bags.

Find the Wikipedia link on Google for Frankfurt Airport, then scroll down to the map and then to the list of carriers that use the airport. The latter gives the terminal normally used by each airline; there is no guarantee that your flights will actually be to and and from the designated terminal, but most are. This should give you some idea of how far you will have to walk once you arrrive at Frankfurt. It will also give you a clearer idea of your route between arrival and departure gates. (For example, both Delta and Czech Air are listed as terminal 2D.) At that hour of the morning, crowds should not be a problem, at least not compared to a couple of hours later.

Roy, the Frankfurt airport does have dedicated terminals for the various airlines. They don't ever change unless there would be some kind of emergency. If your airline is listed as using terminal 1, it will always be terminal 1 and never terminal 2. A gate is not usually designated though, until shortly before landing. I just go to the arrivals page or departure page for the Frankfurt airport and find the airline I am looking for. No need to go to Wiki. Just Google their website. Alternative is to Google your flight # and airline. This will show the status of the flight, if it is on time, and of course which terminal. It is obvious that you haven't been to Frankfurt airport very often at 7:00 in the morning. This is a very busy time there. In fact there aren't any real slow times at this airport.

Thank you all for your replies. All of them helped immensely. I am going to book the 9:10 am flight and as a precaution I am going to only take carry on baggage, which is a huge sacrifice for me. By carrying my own luggage it will save me having to go to baggage claim then to the passport center.
This is my first time using this forum and I will be back in the future. I can't believe how fast you all answered my questions. Thanks again.

Robbie asked a question and I provided an answer with information that I have found to be accurate and useful. It is true, I haven't been to the Frankfurt airport often, at least not in the past 40 years. My only fairly recent arrival there was around 7 or 7:30 a.m. about five years ago, but the airport was not crowded then and we were on our way in less than a half hour. (Our departure, about 10 or 11 a.m., 10 or 12 days later, was a different experience, with large crowds everywhere and lengthy slow-moving lines due to two very thorough security checks.) Others may have a different and more experience, but my statement would apply to vitually every airport I have seen: crowds are nearly always less in the early morning hours than at mid-morning. Also, my use of the qualifer "no guarantee" means the same as Jo's exception for "an emergency." We are saying the same thing. In any case, we are in agreement about Robbie having a good chance of making the connecting flight.