Honestly, that's just an oversight on my part. I'd thought that I went back and removed a few ranks from Balance and other skills like that, ones I don't need so many ranks in, to add Search, but I guess I forgot to. I also thought I had the Wand of Detect Magic in SGT 5 (because I really should have...) Though, the Bag of Tricks should help out in this encounter seeing as how I completely fucked this one over. 
Yeah, I assumed lack of Search was a mistake, and didn't notice Bag of Tricks but CR 4 repeat Fireball traps still basically can't be beaten except through hope and guessing.
?? Are you looking at it? No. So you are averting your eyes, and fall under the 50% rules. Do you have your eyes closed? Then you can't get 100% protection. Looking at a mirror image doesn't cause the gaze, but it does quite clearly also not protect you from the gaze you would otherwise suffer because it is very specifically "averting your gaze" it's in the example of averting your gaze. Merely declaring that you are attempting to use a small hand mirror does not grant you magic immunity to something that you would otherwise have to roll if you had your eyes open, but declared yourself to be not looking at the Basilisk.
Where in the rules does it say that, when looking at something through a mirror, you give it concealment? How much concealment? I looked for a rule like this myself, but couldn't find it, and so I went on assuming that you attack as normal when "aiming" via reflection.
When in the rules does it ever say you can aim by reflection at all? Give you a hint, it's an example of "averting your gaze." The rules for concealment are in the gaze attack section, where it makes clear that for averting your gaze, you attack as if it has concealment.
It waits around the corner. Of the desert. Explain to me how that makes any sense to you. No, I interpreted "in it's burrow" to mean in it's fucking burrow.
Great. Now be slightly smarter than the average idiot and ask yourself if burrows are 2ft depressions, or actual holes in the ground that make turns and go past where you can see.
1,
2,
3 You do not appear to have line of effect to any of those burrows, merely to the opening, try again later.
I guess I figured it couldn't see into the material plane from the ethereal (from the SRD, "Phase spiders dwell and hunt on the Material Plane"). Hmm. That's a good point, I don't know how I'd rule this given that information. Is that true?
Well how do you think it manages to coincidentally go Material right next to you and get the surprise round if it can't see. The part you want is in the
Etherealness special ability descriptor. Specifically, "An ethereal creature can see and hear into the Material Plane in a 60-foot radius, though material objects still block sight and sound."
EDIT: Want to be clear about what an above poster said. Yes it can "only stay ethereal for 15 rounds" in the sense that at some point during those 15 rounds it has to spend a free action and a move action starting it over. But since you can't even move faster than it's move speed anyway, it will just follow you, always keeping you within 60ft at the end of every turn, and if it loses you, it just has to run under the ground/behind a rock to refresh, and start hunting again. I'm going to call it a loss for the Factotum if his response to Phase Spider is to start sprinting in one direction and never ever stop or pass go or collecting 200 dollars.
Yeah... I'm stunned that there's no range/attack given. I filled in the blanks with it and called it gospel, to the point that I was certain it was range touch/touch attack, but nothing is given. lol. There's not even errata, a sage's advice, or FAQ for it. In the interest of trying to avoid shady rulings, and to offer an excuse for why I didn't do that, let's call it range touch/touch attack. I thought it was a touch attack, and thus I didn't use it to channel positive energy since I would have such a low chance of hitting it anyway.
I don't know why it would surprise you, the class is extremely poorly designed. You are playing with a houserule for inspiration too, because the Raw is so dumb.
Metamagic Rod of Empower does it for me. Why not Empowered Twinned? Because there is no Metamagic Rod of Twinning. 
So, no I don't have any illegal spells. Why do I want Fireball and Scorching Ray? Fireball for large groups of mobs, both of them just so I have another chip on my shoulder (helps to balance out that I'm using Alter Self and Polymorph).
Well 1) You should probably clarify that under spells prepared (IE, that you did not prepare Empowered Fireball, you prepared Fireball, and you'll have to take a move action to put away your Bow if that's what you are holding, and then another to pull out your rod of empower). 2) You should probably replace Scorching Ray with Lightning Ball, unless you are really concerned about Ref saves.
Hmm... good point. I assumed Disable Device +20 would be more than enough for this sort of thing, but when half the CR 10 magical traps in the SRD are 9th level spells with search and disable DCs of 34... well, a) that's pretty bullshit, and b) you're right there's no way a trapfinder can bypass these through conventional means. Stupid. I suppose we'll send some lovely little critters from the Bag of Tricks through the hallway and hope it's enough.
Yeah, as long as the first symbol you run into isn't a death, as long as you are willing to take several hours to make it down a hallway, you can totally do it with a bag of tricks. Might want to rest, Prepare Dimension Door, and then go, it will probably be faster than Bag of Tricksing.
Except the Factotum has +22 to hide/move silently? And the Fire Giant suffers appropriate distance penalties. I should have no problem sneaking up within charging distance.
I read the level 5 numbers for this part.
The Gray Render typically has a +20 mod, but with Brains Over Brawn it now has +25. Putting us on equal terms, except that for the Fire Giant to pin me he'd have to do nothing but attempt to grapple me, whereas I can just Bite him, something I would normally do anyway, and get two free grapple attempts per turn. I thought all of this was pretty clear in my analysis.
? So... learn the polymorph rules then get back to me? You have a BAB of +7. Grey Render's have a BAB of +10. Polymorph does not give you a Grey Render's BAB. Therefore, you have, even after Brains Over Brawn, a +22. So the Giant can win checks, pin you, and then damage you, because opposed rolls drastically favor the side with the slightly higher bonus (compared to assumed 10 DCs).
The Trolls are easy. Empowered Fireball, Empowered Scorching Rays, that's guaranteed to kill two of them if not more. Enlarge Person + attacks of opportunity takes care of the rest. Oh, and sure, I'll Polymorph into something if I get scared. Yeah, I'll get a little roughed up, but probably not bad enough even to warrant using opportunistic piety to heal. I'm confused as to how you have any doubt that I beat them.
A) Empowered Fireball plus Scorching Ray isn't guaranteed to kill two, although that is likely. But more importantly, if the very first thing you do is anything besides Polymorph into a Fire Elemental, you lose, because if they grapple you in the surprise round, or at any point before you Polymorph, you can't actually beat them, and they all start grappling with repeated Rends, and you can't break out of multiple grapples at once. If you start by Polymorphing to a Fire Elemental, you can then rely on Burn to beat them, and sure, throw the fireball to speed things up, but if you polymorph into something that doesn't both do fire damage and beat them in grapple checks, you can't even kill them all.
The Shadows are even easier. Opportunistic Piety (hell, Empowered Fireball has 50/50 shot of killing them all). At an average turning check of 9 that allows me to affect up to a 9 HD undead. More than enough. Average turning damage (or total HD turned) of 16 means that, on average, an Opportunistic Piety turns 3 of the suckers (luckily that's just enough). From the SRD, "If you have twice as many levels (or more) as the undead have Hit Dice, you destroy any that you would normally turn," Shadows have 3 HD, and so even with their +2 turn resistance, any Shadows I turn get automatically destroyed.
Fireball only might kill them if you have line of effect to all of them, and that's only likely to be the case the round after all 12 of them did their surprise round punching, and you'll have to hit yourself too, and of course, You are totally wrong about how Fireball interacts with incorporeal creatures, it has a 50/50 shot against each one, so you'll still have 6 left most likely. Turning is going to be the go to move probably, although, it may be better to start with the fireball after they ambush you, and then start turning, since they don't do HP damage, it won't matter. Which is why I said I'd have to do the math on how damaging the initial surprise round is vs how fast you can turn them.
The Mindflayers I'm sure I can kill in any variety of ways involving Polymorph. I had been entertaining the idea of changing into a Bulette, burrowing underground, and then Leaping out from underneath one. Four claw attacks at +15 each will kill a Mindflayer in one round. Now, maybe the other one had readied an action to Mindblast, but with Cunning Insight I still have a 75% to succeed, and then it's just another burrow + Leap.
Yeah... again, you find out the Mindflayers exist when they both Mindblast you at the same time. Then, they have levitation, so you'll actually want to try to burrow above them to drop down on them instead.
Did you ever read Frank running things through the SGT? He's very clear about the Mindflayers starting out hidden among the stalactites and then double blasting to start things off.
