You're trusting that the schematic matches everything in your unit. It may, it may not. Revisions are often made, and the schematic you have might not exactly match your unit.
Apply enough heat and you can damage anything. Some circuit boards are more delicate than others, and even experienced techs can encounter lifted traces. A quality soldering iron (ideally a heat controlled soldering station) can mitigate this. Ironically, a lower powered iron can cause more damage, as you have to leave it on the component/circuit board longer.
This. I was going to chime in with the same cautions re/ doing more damage with an iron that isn't hot enough due to the length of time it needs to be on the board/component lead.
I'm pretty green, too, compared to most folks here (especially to Ray, who's been incredibly helpful to me in a few other threads), but have done quite a few board repopulations and a lot of kit building. Maybe a couple suggestions, just trying to help..
1. To piggy back on, or maybe clarify, what some others have said, do one component at a time, BUT before doing that, go through, make a list of what you have, and match each one to the existing components on the board first. If the kit substitutes a cap with a higher voltage rating, this way you can make your best guess for matches before doing any soldering, and you have a chance to go back and make corrections. Yes, it'll take some time, and you'll have to figure out a way to keep track, make notations, whatever, that makes sense to you, but it may save time in the long run and allow for fewer mistakes.
2. As Ray said above, I wouldn't rely on the schematic. For what you're doing, the schematic is unnecessary... just look at what's on the board, and replace it with the matched component in your kit. A subwoofer control board I just repaired had two C119s, meaning two different values in two different places, two C114s (also different), an unlabeled resistor, and a ton of jumper wires that don't appear anywhere on a schematic. If I had gone by a parts list or schematic, I may have installed the incorrect components. Just go by what's on the board. Schematics are useful for troubleshooting and analyzing circuits, determining voltage test points, and a host of other things I'm terrible at or don't know much about.
3. Soldering tips, some of which may or may not have already been mentioned...
a) Use a small tip, temperature-controlled iron. I've found, for me, that 340C is good for soldering on boards using 60/40 .031" solder, and 350-360C is good for desoldering/wicking/sucking.
b) Keep your tip ultra clean, shiny, and tinned. Through trial and error, unless I'm quickly doing joint after joint quickly, if the iron has sat for more than a few seconds, (and while it's still hot, of course), I'll dip it into a brass scrubbie, then touch the tip to solder, dip it into the scrubbie one more time, then quickly go to the site. Iron on pad and lead simultaneously, touch solder VERY briefly to tip of iron to aid in heat transfer, then solder to junction of lead and pad opposite the iron, flow the right amount, remove solder, remove iron. All of that takes no more than second or two if the heat is right and the tip is clean. If the solder doesn't melt instantly when you touch the iron to it prior to addressing the joint, your tip isn't clean enough. Try scraping it over a wet sponge, then scrubbie, then re-tin.
c) Desoldering takes a bit more practice. Again, a clean tip is just as important. Then, put a tiny blob of fresh solder on the hot tip before placing on the site to be desoldered. I use a sucker if there's a lot of solder on the site, and I cut a tiny notch in the nozzle of the sucker that sort of fits over the iron tip to get a better seal and stronger suction. Iron on the site, should melt in a fraction of a second, sucker firmly on top, press the button, and remove the iron. No more than a second or three on the site. That should remove almost all of it. The lead, if it's still firmly attached, can sometimes be pressed out with the tip of the iron, but again, don't leave it there too long. I've found that using wick takes some technique, too, but I get the best results with it.. you'll go through a LOT of wick, because once there's any solder on the wick, it can't be reused... don't even try. Clean fresh copper wick on the site, lightly tinned iron on top, watch the solder flow into the wick, and remove after the solder stops being absorbed or two or three seconds, whichever comes first.
ALL of that is way harder to describe than it is to do, with a bit of practice. AND.. I've described what works well for me. That doesn't mean it's the only way, or even the best way, to do things, but the results have been very good. One of these days, I may invest in a desoldering station, but for now I'm content with what I have.