Greetings!
So i went down nearly the exact same path as you on my 500 journey.
I had access and drove a stock 68 500f for nearly 2 years before biting the bullet and finding my own 500 which ended up being a full restoration.
A throughout the many drives and adventures with it i, got a feel for what i would want in my perfect 500 and this gave me time to help me choose and decided on how i wanted to build the best 500 for me.
Drivetrain: More power was definitely a requirement, where i live there's a lot of higher speed traffic, and i seriously needed the power to get up to the speed limit, no one drives under the speed limit here, and i needed a car that can reliably get up to 90km/h in a decent amount of time. This imo was the major shortcoming of the stock 500. I was almost to the point of modifying the stock engine in my friends 500 without even telling him lol!. there were moments that more power was a must. Obviously traffic average speed and road design varies allover the road, but doubling the power for example from 17hp to 30 transforms the car dramatically. Thus i am on the venture of constantly modifying the engine, but a prebuild r2r engine is also a option for many. If your worried about originality, i would say, keep the original engine untouched, and swap in a 650 or larger. Then just include the original 500 engine if you plan to sell.
Transmission: I personally enjoy the feedback and simplistic feel of the non synco box, thus why i left it in, but if i were to daily drive, especially in city stop and go traffic, you are right, a synco box would be a must i would say. I live out in the country side, so even though high speeds are required, im not constantly shifting thru gears, and yes at times it would be handy to have a synco box, im going to ride out the non synco for now.
Brakes: i installed a disc brake conversion on my car; mainly because it tied in with some of the front suspension modifications and it was more of a want, then a need. I found that a properly serviced 500 drum brake system worked decently in the 500. Maybe i would do a dual master cylinder upgrade on a stock system just for reliability sake, but other then that, i dont see the need for upgrading the front unless your doing high speed driving consistently. Just make sure you have all fresh brake hardware, and then maybe upgrade if your not satisfied.
Exterior: I would say go for it, choose the colour you want. Yes you might have a bit of a guilty continence as you veer away from the "originality" of the car, i thought so to as i began to modify and do custom things to the car. I did want to keep it original, but i also was conflicted with building the car that i wanted. The reality came to a few points for me: 1. they made millions of these; so less harm in modifying one to your liking. 2. its not a D or an N model (if i began to heavily modify a D or an N model, then i would have certian reservations). but the F in my opionion was smack dab in the middle as far as non special model raity goes. 3. There is a tasteful way to customize these cars while still keeping their original charm, this is the path i planned to take with mine. All in all, a good quality restoration has value on the resale market, and if done right, and budgets kept in line during the resto, the car shouldnt be a loss if you plan to sell.
Paint: This is where i had conflictions in what i wanted. Iirc my car was originally Blu Turchese, but i just wasnt having it. It wasnt bright enough for me. I wanted a colour that was traditional, but also very bright so it could easily be seen in traffic. I also had and wanted a red interior, and that kinda crossed out red or yellow for me (didnt want a mcdonalds colour car). So the blue i chose was close to the original, but definetly had more pop. When your choosing a colour spend the time, go to dealerships and see what colours you like in person. A car can be painted absoulety anything you can think of. I drove around and visited a few porsche and lamborgini dealers to see what certian colours looked like in person. Then worked my way from there.
Interior: My 500 originaly had the 2 tone red/white as you described. I personally loved the style as simple as it was, it really dates the car to the mid/early 60's and i wanted to keep true to it as possible. I went way overboard with a full custom interior, and questoned my sanity of why not just order some pre-made skins. but it was all for the complete final package. I would suggest in my own opinion, stick with the factory 2 tone, it just works with the car.
so unless they are actually scary might as well keep the drums!
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