Waiting for the rebel rate to drop is a good idea, otherwise you might find yourself overwhelmed. Since it's 1846 the Liberal Revolution will roll around soon, so you might want to pace yourself with new acquisitions and focus on militancy management and rebel control. Remember, military presence lowers the militancy of all pops in a province by 0.20, make use of that by garrisoning your most militant pops and liberal states before the revolution hits.
Don't worry so much about the empty factories, the more you have, the more RRs your cappies will build. Also, at the end of the day, it doesn't matter so much what kind of factories you have, they'll all make some money, some of them will perhaps run at a loss in the early years, but eventually all of them will turn a profit. Sure, it's nice to focus on expanding just the profitable ones and setting up proper chains, but it doesn't make that much of a difference. Keep in mind, that cappies will only expand factories if they can't build any more different ones, translates to, hardly ever.
If you're staying con-mon, which you should as France or just about every other European nation, you can just have the conservatives elected ones your country has been blanketed with railroads and continue expanding profitable factories.
About waiting for your overseas possessions to be railroaded before researching the next tech, really an aesthetic decision imo, I pretty much always wait for it though.
PS: Don't underestimate LZ parties, no other policy will industrialize a nation quicker. As France you have the double bonus of having a LZ/Protecionism party, creating the perfect balance between industrialization and making money, and your pops will vote them into power themselves right away, so no need to do any funny business with the elections that will prolly cost you militancy. I'm actually playing an MP with France right now and really having a blast with them!
