One thing you absolutely will want to do, is find out the LWO status of your guy. If he's negative, then any mare will be OK, but if he's positive, you will need to look for LWO negative mares (don't take an owner's word for this, see the test result yourself) or you will be risking Lethal White foals. I know of a number of minis that don't even look to be pintos, that are LWO positive.
The only registrations that have any value (in the US) for a mini are AMHA and AMHR, I'm assuming that those are what you are referring to when you say he is double registered. If your stallion is 32" at a year and a half, he will be a bit taller at maturity, probably pretty close to 34". If he goes over 34", he will no longer be registrable with AMHA, and his value as a stud will go down considerably. An awful lot of people will not look twice at a stud that is over 34", they worry that the foals will go over height and not be registrable with any registration. The height of the parents is no guarantee when it comes to the mature height of their foals. I currently own a 2-year-old filly out of two double registered parents, both about 32". The filly is already at least 35", so her temporary AMHA registration would be be void, if she had one (her breeder died before she wrote me a transfer of ownership, so the filly cannot be registered).
One registration (I think it's AMHR, but I'm not sure, not being a breeder myself, it isn't something I need to know) will not register a foal whose parents were less than 3 years old at the time of its birth. All foals get only temporary registration, they must be brought permanent at age 3 for AMHR and age 5 for AMHA. A horse that doesn't get its permanent papers for whatever reason is dropped from the registry.
Coarse heads, low-set necks, long backs, and short hips are frequent flaws in minis. The weak hip is often associated with a more upright hind leg, and a very common problem that I already mentioned, locking stifles.
One of my favorite online sites is Marestare. I heartily recommend that anyone that is even thinking of breeding spend at least one breeding season there. Breeding minis is not like breeding "bigs" because there are certain problems (like a foal that can't get out of the sac) that are almost unheard of in big horses. Many of the farms that have their mares on Marestare raise minis, because you really don't want to risk the mare foaling alone.
Another site I like is the Lil Beginnings Miniature Horse Forums. If it has to do with minis, it will have been discussed there!