Unless you're just locked into Harley Davidson performance parts, there's a huge selection of aftermarket intakes, exhaust systems and tuners that would work great on your bike, be kinder to your wallet and help achieve your goals of improved performance without giving up any reliability.
FuelMoto, Vance&Hines, Rinehart, Rush etc. all have components that earn at least a cursory investigation before jumping onto the Screamin' Eagle bandwagon. Now.... no offense to the SE stuff but IMHO you can easily find much better value in the aftermarket space.
Ok, first I want to thank everyone for the replies. I meant to get back to everyone last month and actually thought I had replied but now see that I didn't. Was a hectic Feb. :/ Anyhow I ended up going with Rinehart Slimlines. At first I was going to go with the Rinehart Xtreme Duals but I didn't like how the rear head pipe crossed in front of the oil entry plug. I figured that would make adding oil more difficult, so I swapped to the Slimlines.
I also went with the Screamin' Eagle Ventilator Elite Air Cleaner Kit, Part Number 29400217 and the Power Vision Licence. I had them do a full mapping of it on the Dyno etc. Remember the changes I was seeking was for the engine to run more efficiently, to run cooler. My whole thought that by getting rid of the stock pipes with the catalytic converter in the head pipe, replacing the air breather with one that allowed for more/better air flow and having it remapped that it would run better and cooler.
First, the difference is significant, the bike runs a lot better. It's very noticeable across all gears and speeds. The response and power just feels much better, more immediate and the engine just feels better for a lack of a better term. Now for the caveats. The mechanic after doing the work had a few words for me. He said that set the front/forward head to run richer fuel wise. That I'd notice a smell of fuel if I was idling, which did turn out to be true.
That annoys me a bit but that wasn't the thing I noticed the most. The first warmer day that I was out running the bike I noted that the heat coming off of the front head/front part of the head pipe was significant and it wasn't a warm day it was in the 50's. Made me a bit worried that the heat during the 90 to 115 degree days would be terrible. Not only that, I was worried would this effect would be on the engines durability and running efficiently.
Basically I'm confused as to what to say to the dealership. I had spoken to them numerous times that my main focus was on making the engine run better, cooler and more efficiently. I spend more time on the highways/interstates running for hours at a time and wanted to make the bike more reliable and better running when the weather got hot.
Instead while impressed with how responsive the engine is through the gears/powerband I'm now worried that the engine will fail, becoming unreliable. Not only that, that the heat coming off of it in the summer months will make it unbearable. Oh and the mechanic recommended keeping the EITMS off at least while the weather was cooler.
Anyhow, anyone have any information and advice for me here? Is the engine becoming damaged with the work HD dealership did to it? I'm not fond of sucking up gas fumes in traffic either nor that the heat issue instead of becoming lessoned is now a bit further forward and clearly more there than before. The final Dyno numbers on my paperwork say that the final HP is now 85.61 and the final torque is 104.08, just as an aside. A bit busy the next few weeks but I'll try to check back to read any information posted. Thanks again to those who replied previously.