Hey Jarel,
Congrats on the Magna..... I figured you might appreciate a little advice for it?
The flat spot your referring to is common, but can be easily fixed by nothing more than a jet kit. The best jet kit available is from Dave Dodge. Dave is THE man when it comes to Honda V4's. Give him a call at 704-892-7961. I think his jet/shim kit is around $50 including shipping, and it's extremely simple to install.... like you said, the carbs are right on top, and that's the toughest part! Once you've actually taken the carbs off, it takes literally 5 minutes.
Other's have told you that you need to get V&H pipes... they're pretty pricey. We're talkin damn near $600! Cobra's you can find for about $340. But honestly, give it a little time and see what you like before you jump in to any. And yes, the jet kit CAN be installed without changing the pipes and you will have absolutely NO PROBLEMS at all! Actually, it even livens up the sound a bit.
The stock pipes without the baffles that were on the test bike is not normal sound at all. I've got drag pipes and they sound pretty sweet! NOTHING like the one you rode.
BTW, Muzzy does NOT make a slip on... sorry, but you might wanna check out the SuperTrapp 4 into 2... they're pretty friggen bad A$$! They're upswept 4:2 and sound like a fighter jet! Plus, they've got discs for sound control! Well worth the money.
As far as seats go, I saw that you already ordered a Mustang. I personally like the Corbin a LOT better, and being use to a sportier bike, you probably will too. The Mustang is very big and wide and does not look very well with the lines of the bike in my opinion. It's also higher than the corbin. They're both comfortable, just in a different way. but I've taken 900+ mile days in my Corbin without any problems at all... The Corbin is actually cheaper than the mustang too.... Especially if you buy it used...
http://www.magnariders.com/html/forsale.htm
You'll probably want at the least new fork springs, progressives are only around $50 or so.
When your ready for tires, go with the Metzeler ME880 OEM size front, and you have 3 choices for rear.... 170/80-15 (not the best for two up riding), stock size 150/80-15 and finallly, the one I use is the 180/70-15.
And finally, and most importantly, if your gonna ride a Magna, you've gotta check out this site....
www.magnariders.com.
Good luck with it all.