This is always a tough decision to make for any type of artist. I can't really give you guidelines as far as breaking down the price, but I can offer up some observations I have made over my time in the customizing community that may help. You have to price how you feel comfortable and how much you feel your time is worth, but often times in this hobby you won't make much more money than what you need to stock supplies or make the occasional pony purchase here and there. It really just is not a money making hobby.
Another factor to take into consideration is unfortunately in this community you will probably have to start your prices lower until you get your name out there a bit and have established a reputation for yourself. I am sure it is not always the case, but often times I notice commissioners and people buying pre-made customs are more likely to buy from someone who is established and known in the community. All of us customizers would love to charge the type of money we see Darkhorse customs going for; for example. Darkhorse is a very very talented artist who puts a ton of time and talent into her customs not to mention way way more hair than most people do. She has also been around in the community and has developed a large following, a lot of trust and a great reputation. All of those factors allow her to make much more for her customs than the average customizer. I know I am nowhere near being good enough to charge that kind of money myself. That is not to say that you or I could never get there, because that could very easily happen with lots of patience, hard work and love for the art.
I can also offer you a few tips that may help in in eventually cutting your costs to allow you to make more money for your time spent working. The only reason at this point my money made is not completely dumped into supplies is because I have spent a few hundred dollars bulking up my supplies. I overstock my hair, paint and other items so I have tons of stuff on hand and only have to replace items here and there as they run out; then I repeat the process every once in awhile dumping a large amount to bulk my supplies. This is tough to do in the beginning I know, but once you can it can be helpful. Also do not forget to sign up for all the coupon programs you can at places like Michaels, Jo-anne Fabrics and Hobby Lobby and watch for those awesome sales! I can also suggest as soon as you can afford to buy an airbrush and compressor doing so as this will make your FBRs super smooth once you learn how to use it properly and majorly cut your working time down. You don't need to buy the insane expensive top of the line airbrush to start with while you learn and establish yourself, you can get some pretty affordable airbrushes and compressors out there. I started with a free airbrush my mother in law used for taxidermy and have since upgraded twice as money allowed to a super nice airbrush. Are you using the wire method or a reroot tool to hair ponies? If you aren't using a tool I suggest you buy one or make one as it will cut your time down considerably as well. Hairing also just takes practice, in the beginning I took hours to hair a pony and made a huge mess with hair all over the place and on me, now I can hair a G4 pony in 30 minutes to an hour all depending on how many colors I am using to if I am adding extra hair plugs. Sculpting is something I am still establishing for myself, yes I can do it but I want to be so much better at it than I am right now. I will say apoxie sculpt and a bottle of lotion are your best friends! If you use a little lotion to smooth out your sculpting when it is still wet, but you are done it will cut your sanding time down a lot.
I hope I have been helpful! Seriously feel free to shoot me a PM if you want to talk further or even want some tips on brands and such of things to buy, I am always happy to help. Also remember that every artist does things differently and there is no perfect or right way to do things, you have to find what works best for you. I also feel you need to love what you are doing, that passion will show in the quality of your work.