The fin rot started out as an ick-like spot at the base of the dorsal fin(wich didn't worry me too much as it was localized to the one spot), then became a small hole in the base of the dorsal fin and a lump under the scales on his back.
At this point he had been in a heavily planted 2-gallon for over 8 months, and i had missed a month's worth of weekly water changes, seeing the hole I set him up a heavily planted 10-gallon 80% full with an undergravel and tetra 3i filter. I let him adjust a week, and the hole and lump got bigger.
I started a treatment of melafix, according to the directions for two weeks. During the two weeks the lump stopped growing and he lost the back half of his dorsal fin. I stopped treatment, and the rot was on the pause for about a week and two weeks, then the scales on the lump(wich now extends in perfect half-circle halfway to his belly) turned gray and started to look like a scar.
I have given him a dose of melafix, but it doesn't seem to completely stop the rot. He really gets a good kick off of the melafix, but I have maracyn-two and eurythomycin sitting around also, as his rot gets worse I become split as to whether it's better to risk him suffocating to death in heavy medication, or be patient with the melafix.
I would like to breed him one more time, and he seems that he could get in the mood(when I quit the melafix treatment the first time he built GRAND bubblenests for two-weeks) but I don't want to make a mess.

WHAT SHOULD I DO? Please do not post unless you have seen this type of fin/body rot before.

It sounds like columnaris to me..

http://bettysplendens.com/articles/page.imp?articleid=930

I suggest that any kind of rot be treated immediately with antibiotics.

You need to sign up for something like photobucket, or image shack, and upload your pictures to there.
Then you would copy and paste the IMG link into the writing area of a post with photobucket, I am not sure how to do things in image shack

Bella.. I am just wondering if it may be that parasite like Rich's fish had at the show. Only because columnaris tends to migrate over the head and around the gill area.

SS, is it definately a fungus or does it look like squiggly worms coming out of the body?

Hmmm.. It COULD be.. I tend to think dead looking area = columnaris.
Of course not having any pictures, it is hard to say, I mean, we didn't realize that was anything other than a mismark until Leo pointed it out as a fungus.
In that cause a one two punch of a fungus cure and a antibacterial... However the fungus that Leo pointed out to us is highly contagious, and impossible to cure accourding to Leo..
So.. if that is the case, I would rather it be columnaris.

OK, that doesn't LOOK like coloumnaris.. It does actually look fungal.
I would try Maracyn one and two and maroxy, which is for true fungal infections. Between those three meds, it will treat gram postistive and negativebacteria and fungal infections as well as any secondary infections from the underlaying cause.

does he have any roommates like a pleco perhaps?
it almost looks like an infected wound.
Are there rocks or any decor he could have gotten scratched on?
Take a look.
I agree with the treatment above. But please rule out injury possibilities to prevent any future problems.

Also, I would definitely add some aquarium salt immediately and get his water temp up to at least 82 degrees (raising no more than 2 degrees a day) to stave off any other infections and to help boost his immune system a bit.

You guys! I said don't post unless you have seen this thing before.
Someone on ultimate bettas is saying it could be a parasite.
I would not keep a male crowntail with anything but invertebrates in less than a 20 gallon.
The subject of medication to me is touchy, because I haven't successfully medicated a fish with anything but psuedo-medication like melafix.
Can melafix be used all the time? Would it be ok to have a minor diffusion in the breeding tank before a fresh brood?.

AND MOST IMPROTANT DOES ANYONE THINK THAT BY BREEDING HIM BEFORE I MEDICATE HIM THAT I RUN A SUBSTANTIAL RISK OF LOSING THE GIRL AND/OR ALL THE BABIES?

I am thinking of trying your marcyn one, two, and maroxy, and maybe some anti-parasite food, but I know when I do this he will get worse before he gets better, and he might not make it out.

Please understand, it doesn't matter if any one has or has not seen your fishes problem before.. we are going to try to help.
Further, there were no pictures at the time you posted to be able to even ascertain if what your fish is suffering from was something someone had seen before or not.
You saying do not post if you have not seen this when there were no pictures, is like telling someone to close their eyes, and THEN critique your fish.
This is an open forum, and as such, any one may feel free to post in reply to any other post made on this board.
Please understand, and respect that.

As for breeding an ill fish. I believe that doing so greatly increases the likelihood of the male dying from the stress of the breeding, of the female getting infected by whatever the male is ill from, and for the babies, IF they do not die, they could become asymptomatic carriers of whatever issue the father has, whether parasitic, bacterial, or fungal, causing them to be aquatic Typhoid Mary's, and endangering the fishrooms and breeding stock of those who ended up with them in their possession.
In other words, I highly recommend NOT breeding the father until he is well.
As for melafix, some people have had good results, some people haven't. I know some people claim it makes their fish sterile.
I do not know if you can continually use it.
However, as tea tree is not something natural in betta environs, like Indian Almond is, I would not recommend constantly using it.

Well, IMHO, parasite is a good guess. Thing about people posting their opinions is, there could be several people that have seen a similar thing. Nobody here is a PHD with a lab to particularly isolate something every time their fish gets sick. They will share with you what they have done in the past. As for melafix, it is one of the more harsh medications. I only use it on rare occasions to aid in healing fin damage immediately after it occurs. Breeding a fish that is injured is definately not recommended. Not only is there the chance of the cross-contamination of infection, there is more chance of the female killing the male in a weakened state.

I didn't mean to sound rude, and I do appreciate opinion, but in my experience incorrect medication is more likely to kill the fish, because the stress the medication puts on the fish can lower their immune system, and then the infection/parasite/fungus can over-run the fish way faster than if not treated at all.

Hence why the first recommendation is salt and heat... always. To boost the immune system.

Salt is one of my regular conditioners, yes I agree medicated dose of salt and heat then; what? Marcyn one, two, maroxy, and parasite food at the same time? That would kill him I'm sure. So then what order could his system handle each medication, and how long to re-cuperate between different medications? In the ponds these fish live in, they encounter and thrive along with bacterias and parsite, and I imagine even certain funguses that are healthy, when you kill a certain amount of those things other things, nastier things tend to come along.
I understand it's a really bad idea to breed him now as I just studied him and as he bent he would do some horrific tissue damage on his back(makin a mess), but what now? He is already salty at a ratio of 1/2 teaspoon to 2 gallons of water and is at 78 degrees F.

....And he had the salt and heat at the time of the infection and for months before.

I would bump him up to 80 degrees if you can, and maracyns one and two and maroxy are made to be used in conjunction with each other.
How is his appetite and attitude?
If he is still feeling/acting good, then it should be safe to use those three.
If you are sure it is parasitic, then look into which of these meds are good for secondary infections, and treat for the parasite first, with the meds for infection.

The medication period went ok, he lost almost all of his dorsal, but the grey patch on his sides has scabbed over with irridescense. It now appears his scales are extruded slightly, He is not full of gas as with dropsy. After the 10-day medication with maracyn one, two, and five days with maroxy I put him in a 2.5 gallon with a heavy dose of salt for a half day before returning him home. I know that over-salination could cause a slight pineconing, but they started to extrude more after 4 days in his home tank. Should I be worried?