First, your FFL only needs to fax their FFL, a signed copy is no longer required.
Unfortunetly there's no real 100% safe way to order from the internet, especially from an individual that you do not know.
If he accepts credit card via online transaction services such as Paypal(which is antigun) that would be the most secure way.
With USPS postal money order being the next runner up, where you can get postal inspectors involved should something go wrong, although just like any money order it's pretty much the same as giving out cash (except you put the proper receiver's name on it), recovering the fund is not likely should the seller decide to fraud you.
I don't think it's necessary to mail it registered AT ALL, I would only mail it certified at the very most but even I don't do that anymore.
It doesn't prevent mail fraud, it just makes sure that it gets delivered to the person intended. So if the guy is a fraud what good does it do?
Plus it just prolongs the process since it requires signature, if the receiver is not at home at the time he'll have to wait for the next time it gets deliverd, do this enough times and the mail will end up being returned it to the sender.
I think instead of paying for registered mail, the money is better spent on mailing it priority mail which reduces the transit time by about 50%, meaning less chance of it getting lost. But that's only if you're really impatient though
You need to make sure that you retain the original receipt for the MO in the event that the MO gets lost during transit, and the bank/postal office will be able to issue you a replacement.
I have used USPS MO hundreds of times, never had a problem. Never need to mail it registered.
and Lastly, if possible always buy from an reputable seller. If a deal sounds too good to be true? it Probably is!
Good luck.