Hey, let me start off by saying this site is one of my most frequented visits for DnD/Planescape resources.
In any case, I wanted some clarification, but first a little background. I own all of the 2e planescape items that are published (thanks to svgames for the stuff I couldn't get on amazon), and I have the 3e Manual of the Planes and Planar Handbook.
I have an Eberron campaign going with the same players that I used to play 2e planescape so long ago, and I wanted to take them to the planes once more. My issue is with dealing with some of the changes to the planar pathways, mostly involving the etheral/astral plane adjustments. Below are my questions:
1. Am I clear on the fact that the ethereal no longer connects the inner planes to the prime? What adjustments should I be making to some of the 2e material to account for this fact?
2. I read the house rules for changing the clerics' spell power back to how it was in 2e with the removal of their spell levels. Is this the best idea? I guess I could see some HUGE game balance issues there. Is there some kind of system where maybe we could just alter their power level slightly, like a -2 penalty on diametrically opposed planes, and a +2 on aligned ones?
3. I would really like to allow one or two of the PCs to have unique type races/characters similar to what is found in Torment, and everywhere else throughout the planes. Unfortunately, my group is not very high level, and some of the ECL's don't match up. What do you all think of using the rules in the Planar Handbook and/or just scaling some of the PC's races down?
The reason I ask all of these, is that though I am a very experienced DM, planescape or otherwise, I have had trouble with the 2e to 3e planescape conversions in the past. These three issues above are really my biggest problems, and I just wanted a bit more personal insight than what I have seen offered in the content sections (unless of course there is something I totally missed).
Thanks! 
You don't have to make any adjustments. The example cosmology in the Manual of the Planes is just an example; there's nothing that says you have to use it in your own campaign, or even that you should use it in your own campaign.
I think 90% of us on these boards use the Planescape cosmology with only a few additions or alterations. Most of us like the idea that the Ethereal connects the Inner Planes and Material. The default 3e way makes the Ethereal Plane a lot less meaningful and relevant; I recommend you ignore it.
I think it's a terrible idea, personally. The clerical spell level alteration was a legacy of the 1e adventure Queen of the Demonweb Pits, and it was specifically designed to compensate for that by adding a lot of portals to Material Planar worlds where clerics could rest to recover their spells before continuing on with the adventure.
It was stupid that this idea was continued into all planar adventures, whether they were constructed that way or not. In this case, I think the 3rd edition way is much better; there's no reason divine spellcasters should be penalized more than arcane spellcasters.
You could do that if you want, but I recommend altering cleric spells the same way wizard spells are altered.
Sounds fine to me. If someone wants to play, say, a mindflayer but without an illithid's racial hit dice, I don't see anything wrong with it. For example, in Torment, Fall-From-Grace didn't have a succubus' hit dice or all of a succubus' racial abilities, but she was still an interesting character.
Or if all the players are okay with having one or two members of the party being quite a bit more powerful than the others, that's okay too.