The class you're looking for is the Dragonfire Adept (Dragon Magic) which provides a very respectable breath weapon (especially at high levels) "spellcasting" and some alternate forms.
You'll want to read the dragonfire adept handbook, but possible invocations involve frightful presence, interesting shapechanging, dispelling at will (which is sometimes better than SR) and all sorts of fun with dragonbreath. To save time, read through the builds here until you find one that fits your intentions.
If you want to be huge and tough:
- Dragonborn Rapotoran Cleric 4/DFA 1/Eldritch Disciple 10/Cleric 5
this provides significant cleric casting which nets you divine power (HD = BAB and a strength boost) and Righteous Might, which is a much better way of going up a size category. If you really want to tell puny mortals to cower, be a half-minotaur (LA +1 Dragon 313) or half-ogre (LA +2 dragon 313), will provide. Or start out as an anthropomorphic huge viper snake and paint your scales gold.
Instead, I'll recommend an alternate route. Since you're playing a high-level game, take cleric for your last levels, and make sure you have resources for divine metamagic and persist spell. Every day, cast divine power with persist spell and use miracle to persist giant size (wu-jen 7, castable without XP cost via miracle), Spell Resistance (It'll not be all that significant, but you'll have it), Spell Turning, Girallon's Blessing (For the claw, claw, claw, claw, rake series), and the other suite of spells. You'll be colossal and dragon-magical without needing to invest levels in a race.
Make sure your cleric has access to the hunger domain, which gives you a bite attack, and the domain spell "bite of the king" which gives you swallow whole. Unfortunately, there are no spells worth the cost that give you a tailslap or wing attacks, but your Claw Claw Claw Claw Rake Bite Swallow Whole attack sequence will simply have to make up for them.
As intelligent NPCs, dragons will have a range of personalities and motivations; however, since your trouble is with separating them from ordinary humanoid NPCs, I would recommend playing up the stereotypes a bit to add some distinction.
I will draw mostly from Draconomicon here, since the specified system is 3.5. It has some advice on roleplaying dragons, though a lot more on habitat and things like that.
Firstly, dragons have time. Unless they are acting in immediate defence of their hoard or offspring, there is hardly ever a reason to hurry, and it is better to do something right then to rush. To fill the time between, they will entertain their minds with puzzles, whether benign pursuits or malicious scheming as well as the accumulation of knowledge and treasure.
This also leads to their vanity and arrogance. This might vary a bit more, and some dragons are diplomatic enough to hide this from the creatures they interact with, but when one's life is an order of magnitude longer than a human's, it is easy to consider them lesser. An idea could be to try thinking of ants, or some other insect, compared to yourself. This is probably more prevalent with the ones playing the great game than the copper from the description.
They also will seek fortune and fame from the moment of their hatching until their deaths, unlike most humanoids who would do most of this in the adult/middle aged period of their lives. A dragon's hoard (in terms of monetary value) is it's indicator of status (along with age), and a dragon with a small holding will find itself looked down upon.
Additionally, you can add something more species specific to add a bit of personality between the dragons you do have. I can summarize a few of the canon ones for the types you listed, which you can add to taste.
Copper dragons are pranksters and riddlers, and very appreciative of humour. They are generally good-natured, but can be covetous and miserly, as well as very annoyed with anyone who does not laugh at their jokes.
Green dragons are belligerent masters of intrigue and back-biting. As well as treasure, they have insatiable lust for power and victory.
Red dragons are rapacious, greedy, and vain. So like normal dragons, but taken up to 11. They are the most obsessive treasure collectors, and will know the value and origin of every item in their hoard.
Silver dragons enjoy the company of the lesser races, and will protect those in need, though they are generally fairly hands-off unless there is some genuine need for action. They spend a lot of time in humanoid form, usually as either old men or youthful elves. They are probably closest psychologically to the lesser lived races with regard to time.
I'd suggest using these traits to help distinguish your dragons a bit more, at least until you get to having many dragon NPCs that are interacted with frequently. If you want some additional little things, you could do something like accent your speech (draconic puts the stress at the beginning of words, which could carry over into their Common speech) or adopt a mannerism or two.
For books, you can try Draconomicon, which is where most of the info above is drawn from. The monster manual has a tiny bit, though I'm assuming you've read that. There are a few third party books that also deal with dragons, though they might have some differing views compared to official Wizards products (though as DM, you can change whatever you like). For more general information, I'd look into the characterization of very long lived characters in fiction.
Best Answer
Challenge rating
This makes challenge rating a better instrument to measure how monsters stack up against a party of adventurers than how monsters stack up against each other.
A more precise instrument to measure how a monster-on-monster battle may run is effective character level (ECL). The Draconomicon lists the lowest-Hit-Dice young red dragon as ECL 19 and the lowest-Hit-Dice young copper dragon as ECL 15. Using these figures (instead of the creatures' challenge ratings or Hit Dice or whatever) makes the aforementioned young copper dragon's encounter with the young red dragon very difficult (DMG 49), which, as you've noted, it is.1
But even this slightly more precise instrument is still a club not a scalpel. Determining which monster wins in an unseen monster-on-monster fight should be the DM's call and used to further the plot, making excuses for the lower-powered monsters when necessary to enhance verisimilitude (e.g. "Yeah, the copper rolled nothing but critical hits and the red failed every saving throw--it was amazing; it's too bad you missed it").
"But what are these creatures' actual CRs?"
Dragons' CRs are far too low if all their strengths are played to--each is, at least, a sorcerer engine in a dragon chassis, after all, and sorcerers are already among the game's most powerful classes--, but dragons are much closer to their printed CR if played like big, meaty melee monsters with the default feats from the Monster Manual (e.g. no Rapidstrike et al., no Shock Trooper, no Travel Devotion). It's the DM's task to make sure that the dragon and the environment in which the dragon's confronted are appropriate to his PCs' abilities instead of either slaughtering the party or allowing a legendary beast be unceremoniously assassinated (unless that's the goal).
A customized-by-the-DM wily young copper dragon that efficiently uses all of its resources can, certainly, defeat a straight-from-the-Monster-Manual young red dragon that's down on its luck, hungry, caught unawares, and used to biting everything to death... but either of those could be an EL 7 encounter. It's part of the DM's job to evaluate each monster to determine its suitability. Encounter design, unfortunately or not, is more art than science.