I guess it depends on the weight of the rider.
I weighed 170 when I got my 80 inch 1986 FXSTC and never felt a need to mod the engine.
I now weigh 150 and still no need on my 96 inch.

I had speed bikes and got that out of my system when I turned 29 and got my FXSTC.

 

Here are some pics of my 98 Fatboy with mini apes, very comfortable and I like the look. I swap out the seat, add backrest and bags when the wife rides with me.

 

im just 200lbs and the bike is plenty fast for me. I could get a set of carlinis but would not have the $$ to finish the project. If I go with a set from Hill Country Customs, I can get them wired up, with factory ends, new hand controls new throttle, idle, clutch and brake line for about $700. Should take less than a day to put on.
I'll try and find a better route for that breather line, my goal was to just get it away from the bike. If figured I had the hose line, may as well use it so it would not look like crap.

 

And here are a couple of pics set up for the wife, with and without the bags.

 

You are going to love ape hangers. I put a 4" riser on mine and it really helped my lower back. A hypercharger looks cool but it's not really a performance mod. They don't flow much better than stock although it is a slight improvement. Brakes are never a bad idea. And a fairing will make longer rides less stressful on your neck,and they look cool. Then you can put a stereo in,gauges.
The apes will be your best comfort mod. How's your seat. A mustang seat is always money well spent. My stock seat wasn't bad,at least I didn't think so,until I plopped my rear into a mustang. They are just awesome.
Enjoy doing your mods. It's always fun to wrench on your own bike. It adds the the feeling of ownership. Making the bike yours.

 

Shredding Rubber - always done my own work on my bike, no engine rebuilds or anything.. luckily. Dealerships around here have a shitty reputation and have not had any recomendations for an independant shop. Besides I enjoy doing it.
Yes the brakes make sense...but asa previous poster said... mine work fine so I would just be replacinf for the sake of it. I think I have talked myself into the Apes..I think the fairing is just too much $ to do it right so I'll skip it. I have two seats, my everyday and my long ride one so I'm covered there.

Astark - nice ride man, think I will go a little higher with the apes.
Thanks for all the input.