Meef,
Small cap numbering is weird, but you’ll see a lot of the same values, so you eventually get familiar with what “number” is what. I think the values are in picofarads (.000,000,000,000). The first two are the significant ones, and that third one is the number of “zeros” on the end. So, a 104 is 10, with 4 zero’s or .000,000,100,000. The decrementing values to the right of the decimal are milli, micro, nano, pico or m,u,n,p (the groups of three zero’s). Sometimes you also see ones with just a 2 digit number or something, maybe with a letter. I think they’re all in pico’s.
I’m looking at a print of the Core schematic pdf here, along with that construction page at uCApps. Looks like the cap numbering may be different (maybe from the two added bypass caps). C6 on my print is the 330nanofarad (334). Should be near the big-ass 2200uF cap (BTW- the electrolytic’s are usually the large values, like microfarads, and have the actual values printed on them, along with their polarity). Looks like the 100nF’s are the two small bypass caps which were added (under the core). I’m not sure if Smash or anyone has gotten them into permanent locations now though. There’s also a 100nF(104) in parallel with the 10uF (electrolytic) near the regulator’s output. On this pdf, it’s C3, but on the site it’s C4 and the 10uF beside it is C3. Make sure you get the negative sides of those two electrolytics tied to ground (should be the center pin on the 7805).
As Thorsten says, always go by the schematic. If you’re getting wrong numbering on the caps, just use that and trace back to another PIC pin or something to make sure all the stuff’s where it belongs. The 10uF and 2200uF are the only ones that have to go in a certain direction.
Yes, it looks like the crystal on a Core I’ve got here is inside the socket, and perpendicular to it. Top or bottom shouldn’t matter, as long as it’s got a solid connection and isn’t touching any traces or pads. The short ones will fit under the PIC (my socket was shaved out a bit on the inside for it). Looks like the taller can in the uCApps pictures is underneath. I’d stick electrical tape or some insulator under, or around the crystal if you do that.
You may have been given extra parts the kit, but make certain the ones in the schematic are all present and accounted for on the board (along with the two 100nF bypassers), and the values and polarity are right. Don’t leave any empty holes. If there’s any part missing, you should be able to find one on a broken something somewhere around the house and desolder it. (No offense to the kit dealers. I know you guys are extra careful ;))
I’d check all the traces extra close, if you think you may have bent that PCB. Stick a multimeter, set to “continuity” on both sides of the “suspect” area and make sure it’s not cracked (not sure if you’d have to bend the board again to really check that). If you need to fix it, or want to be safe, you can either bring a long, uncut leg of your component, all the way through the hole, and neatly fold it under the board, in the path of the trace (if it reaches), and solder it down. You can also take a piece of small solid copper wire (maybe tinned with solder), and bend it into the shape of an “L”, with the short half being long enough to bridge the trace. Then you can use the long leg to hold it onto the board where you want it, and tack it down with some solder (don’t get burned). I use one of those two armed alligator clip doohickeys with the heavy base to hold it, but you could also tape it to the board, and bend it into a shape to make contact. After it’s done, you can snip off the long part with some toenail clippers to clean it up.
Sorry if you already knew any of that (looks like you may have done the leg-bridge method).
Hope something in there helps! 
George
