Lots of questions. Let me try to sort thru this for you. If you are only replacing the primary chain guides (the long chains), then there is no reason to take off the short (secondary) chain up top. This means you don't have to take off the cam gears either. And as long as the cam gears don't come off, then you don't have to replace the cam gear bolts. You certainly don't need new cam gears, unless yours are messed up, or worn badly or something. Sounds to me like you're gearing up to do a much larger job than what is necessary to fix your car.
The cam holding tool just holds the two cams relative to eachother. This would be good for when you are removing or tightening the cam bolts, etc. If you're not doing that, then you probably don't even need to use that tool. The D slot plates are for taking two completely free wheeling cams (all chain stuff off the motor), and lining them up relative to eachother. In other words, for setting up cam timing from scratch.
I think the ARP torque specs would be exactly the same as stock, but the sequence for tightening wouldn't need those tighten-loosen-tighten steps. (This is an interesting question though, and might be worth calling ARP tech support about for verification of torque spec). Definitely get the ARP crank bolt, but you shouldn't need the cam bolts, since you don't need to take the cam gears off unless they're bad.
The trigger wheel is a black wheel about 6" in diameter, that has "teeth" on it. The crank sensor (located in timing cover on the side) sees these teeth go by, and that's how the computer knows where the engine is in it's revolution, and also how many RPMs the motor is turning. They normally aren't bad, but in some race motors there have been reported problems of them cracking. Autofab makes a billet aftermarket one for maybe 80 bucks or so if you want one. Just make sure it goes on the same direction it came off, and don't forget to put it on before putting the timing cover back on.
With the cover off, the crank seal can be tapped out easily. Before you remove the old one, simply look at how deep it's installed. Flush, if I recall, with the front of the timing cover. Tap the old one out, tap the new one in, and try to get it nice and straight. The factory tool just lets you smack the new seal in without thinking, to the exact depth and straightness every time. Not a necessity if you look at how the old one is sitting in there, and just take your time to tap the new one in the same spot. I did mine that way, and it didn't leak a drop. It might even have a flange on it, to set it's depth, but I just don't remember. I also don't remember if you're supposed to use a thin layer of silicone around the seal... I don't think so.
The timing cover just unbolts. But don't forget to unbolt the 4 studs/nuts on the BOTTOM of the timing cover, coming up from the oil pan. You'll need a new timing cover gasket set and some black silicone for where the different edges of things come together. Read the factory manual for instructions on where to dab some silicone.
The oil pump is at the front of the crank, and the pickup tube runs from the pump, back to the rear of the pan. The tube and pickup assembly are one piece, if I remember right. You would need to be careful to make sure that the pickup is at the same depth later as it is now, so it doesn't get angled away from the pan. I really don't think you need to do this. They're worried that if the plastic pieces of the guides clog up the pickup, the motor would starve for oil. Chances are that with enough oil changes, these pieces won't present a problem. If you're worried about it, you could pull the pan and just clean the pickup tube right where it's at, and not have to risk screwing up putting it back on wrong or something. Most of the plastic pieces probably come out with oil changes anyway. The rest that makes it thru the pump probably get caught in the oil filter, which does a great job of filtering oil. Nothing large will ever get thru an oil filter. And I've got news for you. If you have a 96-04 modular motor car, you have to pull the K-member while supporting the engine from the top with a cross brace, in order to get the oil pan off. NOT an apartment complex type job. If you've got good oil pressure, I wouldn't worry about it. And if you do have problems there, you also have to replace (cannot clean) your factory oil cooler, which is the big round piece the oil filter bolts to. It's probably $200. So you're getting in deep, trying to do that job. Don't get into any of that oil pump stuff if you don't have oil pressure problems. Verify problems by putting an aftermarket oil pressure guage on the car and make sure the pressure doesn't dip at wide open throttle.
Back to the chains, if your only problem is the guides, then I would just put the motor at exactly TDC on the compression stroke (you can use the OTC tool kit's crank holding gear to do that, or a long screwdriver or TDC finder). Then I would take the balancer, timing cover and trigger wheel off, and then paint a mark on the cam gear and timing chain, and then again on the crank gear and timing chain. Unbolt the tensioner, unbolt the guide and replace, replace the tensioner, and pull the allen wrench, which snaps tension on the chain. Make sure nothing moved, and the paint marks still match up, and you should be good to go. Reassemble.
Notice the bottom timing cover bolts...
Oil pump pickup tube partial picture:
Here's a side view. Notice how my screen has junk partially clogging it? That was not enough to cause an oil pressure problem. These were actually paint chips from the oil pan. They got there when the Vortech supercharge was originally installed, due to having to literally poke a hole in the front of the factory oil pan, in order to tap it for a return oil line from the blower. What a crap deal. That's why in the picture of my Canton race oil pan above, you will notice I had a pipe thread tig welded into the front of my pan, and then a -8AN fitting screwed into that, so I could run quality race hose up to the blower instead.
Trigger wheel installed:
Trigger wheel closeup:
You should also know that you will need a harmonic balancer remover/installer tool, and a power steering pulley remover kit. You cannot do it any other way than to get the balancer and power steering pump and pulley off. Water pump can stay on. Belt tensioner can probably stay on.
There are so many things you can do to your car to get more performance out of it, it isn't even funny. Way too much to list here. But you're barking up the wrong tree so far. If your ignition parts are bad and you want to upgrade to MSD wires, fine. Use stock Motorcraft, or NGK plugs. Ford Racing or MSD wires. STOCK coils. Shorty headers are good, but rather hard to install. (Although if you do have to drop the K-member and pull the oil pan, this is THE time to add headers!). This must be done on a lift, and isn't easy. Installing turbos would be a rather huge, expensive deal. Not for the budget-conscious, trust me. If you have any hesitations or hickups at around 3000 rpm at full throttle, clean your IMRC plates. Install a cold air intake tube and K&N filter. Clean your MAF meter if you haven't before. The best gains you'll get are going to be from just getting your car running 100% factory right, and then adding exhaust upgrades and an SCT chip.
PM me if you want, since selling race parts and tuning Mustangs is what I do.