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A quick eBay check can confirm my statements, so I'd say that in excellent, near-mint condition, the minifig Jango Fett could fetch up to $70 alone. The lowest I have seen are around $50, not bad considering that is what the set he came in originally retailed for. I'd have to see the severity of this chipped head, but that will definitely lower the value. The quality of the printing on his helmet is another factor to consider, but not one as heavy as damage to the figure. The "incorrect" arms you mention might be a effect of uneven coloring on Lego's part, so that won't be a huge detriment, but I'd have to see it myself to be absolutely certain. All in all, you Jango Fett figure is probably anywhere from $10 to $40. Boba Fett is also worth a pretty penny; I'd say slightly less than Jango. Assuming yours is near-mint, it could be $30 to $50 in value.
Now, since the set is complete, value really comes down to nitty-gritty factors like how clean the bricks are, wear along edges, luster, etc. A big factor in this set is the brightness of the white bricks. This set has a lot of white bricks, so you had it exposed to sunlight for a long period of time, the white will start to show signs of yellowing. Yellow bricks are a big turn-off to collectors, and will therefore hurt the value immensely. I'm an optimist, however, and will assume your set shows none of the yellowing, and aside from some dust and the occasionally dirt splotch (easily cleaned), looks more less exactly as it did ten years ago. I will say the set itself is around $80 in value. The ripped instructions don't really make an impact here, as long as they are complete and useable. The missing cover is upsetting, but not critical since all it contains is the box image and the page to assemble the minifigures (anyone can figure that out).
Now, for the grand total. There is a kind of "bonus" for having both figs and set in one package so that combined, they are worth more than just adding up the values I gave you. To cut to the chase, then, I value your entire set at a range from $150 to $180. You might see MISB copies go for triple that, but even at the low end, your set has still tripled in value. Not bad, but then again, all of those sets from 2002's Attack of the Clones lineup are good investments. Pat yourself on the back!
Did some research and I have the right arms for Jango. It's just the small paint chip here and the face damage there, that bothers me. Oh, and the fact that one of his legs are crushed (how I didn't notice that at first is beyond me). It's good those aren't pricy on Bricklink.
You also said that some of the AotC sets from 2002 were good investments. Which ones exactly?
The 2002 Attack of the Clones line-up had some real gems. The most note-worthy ones are:
Tusken Raider Encounter - A simple set that is the lead-in to Anakin's massacre of the Tusken Raider village. It was only a small, $9.99 set at the time, but the inclusion of two (!) Tusken Raider minifigures has made this set's value shoot through the roof. The Tusken Raiders, obviously, were only ever available in this set.
Bounty Hunter Pursuit - This was a $30 set with two really nicely-designed speeders from the chase scene on Coruscant, but of course, the price is driven up by the presence of another rare minifigure, Zam Wessel. No other set contains her, and as an added bonus, a non-flight headset version of Obi Wan Kenobi is included as well (this is not the same as the one included in the Jedi Starfighter set).
Super Battle Droid - For a Technic set, it is way better designed than the Jango Fett model you own. It features a lot of click ball joints for increased poseability and a lot of BIONICLE parts in light blue and metallic blue colors. This is the only set to find such colors.
Jedi Duel - If you are not into flesh-faced, cartoon monstrosities, this small set is the only set to feature Darth Tyranus with a uniquely-colored speeder bike.
Overall, these sets are worth a lot today because they are well-designed (the first big renaissance in parts development, coloration, and assembly since the inception of the Star Wars theme), have extremely unique minifigures, and (of course) carry the "Star Wars" branding.
Back on topic:
*squeal of happiness* I think I will be making some good money in the future. MUA-HA-HA-HA-HA!
Maybe a valuation of Jedi Duel and Tusken Raider Encounter are in need as well.
(can a mod change the name of this thread to "Request Valuation of SW Attack of the Clones Sets"? Thanks.
Anyway, back to the sets; they really set the stage for all the great things to come from Lego Star Wars. Blocky designs firmly became a thing of the past. Heck, you need look no further than 2008's Clone Wars line to see how the 2002 set designs still heavily influenced the look and structure of sets like the 7676 Republic Attack Gunship. Those sets were so advanced in some ways that today's sets lack; in exchange for neat, useful features like retractable landing gear, storage space for accessories, or printed parts, we get foot detailing on minifigures, flick-fire missiles in every available nook and cranny, and stickers galore. It's just not the same, but we can't live in the past now, can we? But we can treasure these gems.