Before I get into a bunch of explanations about parts you swap to improve your combo, first I want to say again that you are not getting the full potential out of your car. On the high side, you're going to pick up around 15rwhp from the MAF/TB/Intake swap. That's only good for 1.5mph and maybe .15 in ET. I'll bet that your timing isn't quite right. You should be at ~14* timing. Get a timing light. Make sure you're running whatever fuel you always fill with. 93 octane is preferred for performance. Hit the track and make sure that each time you run, you are running at the same motor temp to ensure consistency. Start at 13* and bump 1* at a time. Drive it the same way every run. Watch for a difference in trap speed. When it stops going up, back the timing to wherever it reached the top trap speed and leave it there.
What they're saying about slicks vs. drag radials is not technically incorrect. Slicks are bias ply and some, the majority, have very soft sidewalls that absorb shock to the tires. Manuals tend to shock the drivetrain because the instant connection of the clutch causes a spike in the amount of force that is sent to the rear tire. At that point, either the tires break loose, or there's enough traction to hold the force and the drivetrain must absorb the shock. With slicks, the traction is there but the sidewalls allow some twist that absorbs some of the energy and spreads it out over time. This has a spring-like effect that reduces the spike of force. That said, going with a slick loses you the ability to drive with nice traction on the street, and it also will be slower at the track vs. a drag radial that hooks. That's because the drag radial has lower rolling resistance that I mentioned before.
Next, you're interested in knowing why trap speeds are not as affected as ETs by driving and traction. Make no mistake, trap speeds are affected by both, but the difference is that if you sit and spin off of the line, time is elapsing, but distance is not. That means you still have just as long to accelerate and when you start to hook, you're still have almost as long to go. Think about it this way at your power level, like my Black Jack, at the end of the track, you're only going to accelerate by about 2 mph through the last 60', which is how they measure trap speed. So no matter how bad you screw up the first 60', you'll never see a difference of more than 2 mph. Whereas, you could easily see a 1/2 second difference or more from a bad launch.
Put your intake on, and go with a quality mass air meter. With 3 combos, I've run the 75mm bullet from Pro-M without issue. Just make sure whatever MAF you run is tuned to the size of the injectors you have. I would recommend 24 or 30 lbs injectors. 24s will be plenty for your power level, but 30s will give you room to grow. The stock 19s may get the job done with more fuel pressure, though that makes it hard on your fuel pump and is not what I reccommend.
With your new intake, MAF, and heads, the stock throttle body will then be the most restrictive part of the intake tract and is absolutely worth some power. Those saying it wouldn't help are probably thinking about a stock intake that only has a 58mm opening and doesn't benefit from a bigger TB. A stock explorer intake has a 70mm inlet and should be matched to a 70mm TB. However, some people choose to open up that port with a die-grinder and install a 75mm TB. If I were you, I'd just slap it on as-is and add the 70mm TB when you can afford to.
A 3.55 gear is a great street gear. It gives a big advantage over the stock 2.73 gears, and one nice thing is that a 3.55 can have an exactly matched speedometer, but they're a compromise at your power level if you want the best 1/4 mile. You want a gear that puts you through the traps at the very top of 4th gear. For you, a 4.10 is just about right, and you will likely end up growing into it. Will it make a 2-3 mph difference? Yes, it probably will. For one, launching out of the hole will be much easier with less chance of bog. Two, you'll be able to go through the traps somewhere in the sweet spot a little past your HP peak (52-5300rpm). You'll end up trapping at 5600-6000, which is just about perfect.