Warranty Company saying neglect, so now HD saying 3400 out of the box just looking at my options. Can i just pull and replace or do i have to "open her up"?
I think my first action would to the warranty company - "prove I failed to maintain my trans"
You ran it with no oil for 5000 miles? It will have evidence of overheated components. Did the dealer measure the measly 20-24 ounces of fluid that comes out of the trans when you drain it?
And shame on your dealer for even raising a flag on this.
I think my first question though is, who is the warranty company? Is it the Harley program purchased from Harley through a dealer or is it an aftermarket program that the dealer is selling that has no affiliation with Harley?
Just some thoughts to ponder.
You could just have the trans rebuilt stock.
If you go with the SE 6 speed gear set there are mods done to he trans case that are irreversible, e.g. you have to grind away portions of the case that are needed for the stock gear set.
You will end up with a 6 speed that has no increased value for trade in (up to you if that is important). That also means you end up with one of the many just about useless 5 speed gear sets that are laying around.
There are probably a couple dozen of us that have those 5 speed sets in our garage/basements.
If you go with the the Baker DD6 you always have the option of putting the stock 5 spd gear set back in if and when you go to trade in the bike (although not in your case unless you buy someone's used set). Then you will have the satisfaction that you are not losing on the trade but end up with a 6 speed gear set that you may never sell. Although, just as there will always be a market for older bikes, there will always be a market for parts. And in this case, my guess is that there is a potentially bigger market for a drop in 6 speed.
The Baker option also gives you the option of different comp sprockets sizes. You can go with the standard set which will keep your overall ratio (and 1st) close to what you have now, with the addition of a DD 6th you can drop the comp sprocket down 1 or 2 steps, effectively lowering (higher numerically) the overall ratio.
The DD6 will give you about a 400 rpm drop in 6th, 1 size down gives you about a 200 rpm drop and 2 steps gives about 0 rpm change in 6th.
After a year of using mine I dropped one size. The 200 rpm drop in 6th is nice but I like the overall ratio now better. It is better suited for the way I ride in the mountains. Prior to to the change I was constantly hunting for the right gear in the 2-3-4 range. After the drop I found I was much closer to the rpm range I wanted to be in to match my "comfort" speed.
But, back to the first question, who is the warranty company. And before you spend any money I would strongly suggest you research and read the Magnuson–Moss Warranty Act, literally an act of congress, that protects consumers.
http://en.wikipedia.org/wiki/Magnuson%E2%80%93Moss_Warranty_ActIt is incumbent on the warranty company to prove you failed in maintenance, not the other way around. It is this same law the does not require you to use the services of a selling dealer or to even keep receipts of maintenance.
Been there and done all that, on both sides of the equation.
And don't worry about pissing off the dealer, sounds like you should be looking for a new dealer anyway.