You are asking for a ton of information. Back in the days of friction shifters we could pretty much mix and match anything. Today there are variances in dropout widths, cable pull requirements and bottom bracket shell variations. That's the bad news. The good news is we don't have to fret over French threading anymore.

My first question is "What are you thinking that you want to improve?" Honestly, even low end components today are really pretty good. The performance range from the cheapest components to the most expensive stuff is really pretty narrow. Prices as you move up the food chain, however, escalate at an exponential rate. You can spend a ton of money to achieve a very modest, if any, performance benefit.

You used the words "as finances allow." How much do you suppose Trek has to pay Shimano (or whoever) for a rear derailleur? Now now much do you think you would have to pay for that same new part? As a general rule, a frame set plus all new separate components will cost the consumer much more than buying the equivalent brand new complete bike off the floor. You get the satisfaction of getting exactly the parts that you want and you get the satisfaction of doing it yourself, but you aren't going to save any money. In fact, it's probably going to cost you significantly more money.

I've been fooling around with bikes for a lot of years. I started when I didn't have ANY money and I actually used to prowl the subdivision on garbage days to look for other people's cast offs that I could salvage parts from. My bikes have gradually improved over the years but, honestly, my performance has stayed relatively about the same. The people that I used to struggle to keep up with I still struggle to keep up with.

Once you get over about 15 MPH, air resistance accounts for over 50% of all the factors that are holding you back. As you speed up from there, air resistance becomes an increasingly dominate force. If you want to go faster, work on your position on the bike. If I were starting out today, I'd spend less effort and money on componentry and more on my positioning on the bike. I've never had a professional bike fit but, if I were starting out today, I'd definitely spend the money to get one. I think that would be a much, much better "bang for the buck" package than a higher end drive train.