The 07 manuf. license is will cover manuf. and dealing,  the SOT covers all NFA manuf. and dealing except Destructive Devices, but even then you can transfer and deal a limited amount of those, since DD licensed FFLs are so rare due to the costs.

There is no manuf. fee for each item, but if you produce over 50 firearms/year then you will have to pay excise tax on those firearms.

Apply for your FFL-07 now, as it will take till june to get it approved, the SOT is due July 1st so if you get your FFL later than July you have lost that much on your SOT tax year.

There will be plenty more questions you have but your local ATF inspector will answer all your questions in your approval interview, or any time you call them up with questions.