Seat covers aren't going to hide or cover the smell, you will need it professionally cleaned or need to replace the foam and covers. That smell will also be in the door panels, and head liner. You have a better chance of having the dogs cover up the smell, but they are just going to add to it.
Not sure why you think aftermarket alternators are sketchy. If you are going to get one, you just need to know what RPM it gives full rating, and what it gives near or at idle. A graph is best. There is no problem with a known dealer, the problem is buying a cheap alternator off
ebay to save $50 and not realizing that it doesn't give that 300 amps until 3300 rpm, (which nobody cruises at), or may even give less at idle than your factory that was half the max amperage, because they did some cheap *** rebuild. After saying all that, you don't need one. Your fuel injection and AC pull about the same amperage a small amp will. If you start doing other things, where you want to add extra lights / light bars, increase your stereo beyond where it is, add auxiliary circuits, then you would want to increase your battery and alternator. Your alternator looks like the small 105amp to me, but I could definitely be wrong. You can buy 105, 130, 145, & 160 amps from the auto parts store for $150-$200. You might get a little light dimming with your current setup (with lights and AC on), but wait until after you do the big 3 upgrade and see if that solves it. You might want to upgrade battery and alternator after that, but I doubt it, and would only think about it when you already need to replace one of them.
If your head unit did 50w RMS, I would say no you don't need one, but I would get a small amp. If that head unit is new, id even take the 20-25% restock fee just to buy a different head unit and you will save the money from buying an amp.. One last time, I would still also spend the $50 and get rear speakers, (before you buy an amp so you could match it up.. and not have to buy another one, but it sounds like you will just live with it). Your spending near $1000 on your system. To add rear speakers before you buy an amp means just buying the speakers. After you buy the amp, it means getting a new amp too, ($50 vs $50 + $100-$150). I'm curious if anyone who tells you not to buy rear speakers knows how low the door speakers sit in this truck (calf to knee height), and how they are easily blocked. Your speakers are so low wattage, you could get away with the factory wire just fine, but if you are using an amp, that means you would have to mount it somewhere to cut it and splice in, which won't work. Just run new speaker wire from the amp, (14-16awg is plenty for the door speakers, I'm sure you could go even smaller, but I wouldn't just because of: when you feed it through the door gap, the cost difference is minimal, and it wont hurt to go big.
The panels come off easy (theres youtube vids if you have never done it). The hardest part will be going through the door gap. The boot connector has a separate clip on each end, Just take those out, and use dialectic grease to pull the wire through, and to reinstall the clips and boot.
Sound deadener is something you can do later if you want, but doesn't sound like you will. Its about getting rid of the ambient noise when you are listening to your stereo, or when you are not and you don't want to hear everything else. That won't cost any thing more or less or take anymore time or anything if you do it later.
