Im really sorry to hear about ya troubles, but to be quite honest, im going thru the exact same thing....here is where im at:
I ordered a 10" over stock, underbraced swingarm in a raw finish (as i wanted to powder it to match my bike) for my 2004 busa from Johnny Rocket swingarms on Ebay. After about a month, i recieved a BLACK 10" over stock, OVER braced arm, so i quickly contacted JRS (we will shorten Johnny Rocket Swingarms for typing's sake) to correct the error. This being back in January, they said to send it back and they would get the correct one out to me. After shipping it back to them (ON MY OWN DIME), i had yet to hear back from them for over a month. Finally i was told that my swing arm would be arriving by the end of january. It didnt....
After about 5 emails NOT being returned i found them again on ebay and left them a message on the number listed. About a week after the VERY unpleasant message i left, i recieved a call from the owner stating that a previous employee had been ****ing the company over and stealing customer's money while not sending out the product (mine being one in that category supposedly). The Ownder of JRS then stated all his underbraced "cores" were out of stock so it would be 12 days before one came in, plus another week for shipping. Well after TRIPLE that time I finally recieved the (seemingly) correct 10" over stock, underbraced, Raw finish arm.
After a couple issues at the powdercoaters, i finally recieve the arm back 2+ weeks later, but at this point i dont care, since my bike is almost done (and its been in pieces since i wrecked it off a cliff over a year and a half ago)....Well finally after 2 more weeks i have an entire Saturday and Sunday dedicated to simply making my bike whole again when i run into the same problem that you did, i could not get all THREE bolts to line up. JRS actually included an additional "knuckle" when they shipped the swing arm, but that did not work either, so no matter how i did it, i could only ever get 2 bolts in. After waiting another week for lowering links to come in, i then tried again, and it still would not work. The only way i could get it to get all 3 bolts attached is with FOUR inch lowering links, and even then, it was nearly rubbing the undertail. I do NOT want to run a 4 in drop, so i am VERY interested to see how you are able to get yours to work as im just about ready to go buy another extended arm and give a big middle finger to JRS (who AGAIN are not answering my calls or emails, yet continue to get nothing but positive feedback on Ebay).
Good luck getting yours working, and please post any updates here, and im really in the same boat as you. If i can figure mine out, i will let you know as well....I appologize for how long this rant was, but that has been almost 9 FU**ING MONTHS of headaches all comming out at once!!!