In general, Spelljammer is a campaign setting that joins things together by going out into space and Planescape is a campaign setting that joins things together by using multiple dimensions.
Both settings involve movement in different directions, so you may find it a lot easier to build up one crossover campaign setting and then do the other crossover campaign setting later on.
I can give you advice, but remember that this is just ‘one guy’s opinion’. For more advice you might want to repeat these questions to other SJ and PS fans over at the SJ forum at The Piazza or the PS forum at Planewalker.com.
Hmm. I think of different planes as multiple layers of the universe. Each one is actually three dimensional. They all exist in the same space, but are also separated from each other.
Lets flatten the Material Plane and the Inner Planes down to two dimensional planes for a moment, so that I can make a point. Imagine a sheet of paper (the Material Plane) and imagine drawing a circle on it (that is a cross section of Aebrynis, but we will pretend that it is the whole planet). Now stick another sheet of paper on top of of the Material Plane and you have one of the Elemental Planes (Air for argument’s sake). Cast a spell while on Aebrynis and you call down an air elemental. So that implies that their is a circular area on the Elemental Plane of Air that corresponds to the position of Aebrynis.
Taking that further, I see a Watery version of Aebrynis, an Earthy version of Aebrynis and so on. And while these would not be mirror images of Aebrynis, there would be places on them that correspond to areas like Cerilia.
I’m not sure if a BR lay line is exactly the same as a lay line in mythology, but they are basically two dimensional lines of power that move across the world. So if there were lay lines on our ‘flat Aebrynis’, we could probably trace those lines on the Air echo of Aebrynis, the Earth echo of Aebrynis and so on.
Essentially, I would create a set of ‘parallel’ lay lines that are found in other planes.
(I am not so sure that I would extend lay-lines into wildspace, but if you really want to include them, I suppose that stars could be use as objects of power that generate space lay-lines that spelljamming ships could fly into. However, if you do that, you will be generating a thing that is exclusive to ‘Birthspace’. I’m not saying that is a bad thing, but if you create Lay Helms, that take power from lay-lines, they won’t work outside the crystal sphere.)
BTW: Because Transitive Planes connect multiple three dimensional planes together and touch them all, I have come to the conclusion that they must be four dimensional planes. You might want to drop that theory next time you bump into a PS fan! 
Spelljammer can be used for many things, but limiting spelljamming to trade routes would be cutting down on all your other options.
I believe that you should be creating BR inspired concepts that can be used to create asteroids, moons and planets that your BR PCs can go and visit. I believe that you should be creating space monsters that take BR concepts and put a new spin on them. I think you should be creating monsters that take SJ monsters and put a BR spin on them and creating monsters that take BR monsters and put a SJ spin on them.
Have you seen the Adlatum Campaign Setting that the Dragonlance fans created? If you haven’t, you should check it out. It is really great and should have won an ENnie Award.
Well, ‘Birthspace’ is your chance to create your own Adlatum. In fact it is your chance to create half a dozen Adlatums. And spelljamming is your way to connect a ‘distorted Aebrynis’ to the original world.
I’m told that Birthright has rules for mass battle. Well, SJ is a chance for you to have mass space battles.
On a smaller scale, spelljamming is also a great way to do planet-hopping trips from Cerilia to Aduria and Djapar and lots of other places on Aebrynis.
I would suggest you look through canon sources for clues as to how many portals exist and who might have created them.
If you are playing with 3e rules then check out FRCS to see how another D&D setting (that existed when Birthright did) dealt with this.
IIRC FRCS makes most (if not all) portals man-made. But then this is something that the local gods can control, so it would be perfectly OK to have more divine portals and less man-made portals.
Portals create ‘free travel’ between two places and despite the fact that some would be dangerous, I think that power groups would stumble onto others and use them for economic benifit.
FRCS has portals from one part of Toril to another part, so you might want to have some portals that link to place on Aduria and Djapar (instead of other planes).
I suggest you use Planescape instead of reinventing the wheel.
But in general, planes with 3D open spaces (like the Elemental Plane of Air or the Astral Plane) have zero gravity. On some planes, people can use their own mind to will themselves to move.
Planes like the Elemental Plane of Earth are death traps, so unless you have high level PCs who have the ability to ‘burrow’ I would avoid sending them there.
In some ways, Spelljammer is a lot safer to ‘visit’ than Planescape, but if you cherry pick a set of ‘friendly’ planes, there is no reason why you can’t use PS.
Well, I personally prefer 3rd edition, but everybody is entitled to play the version of D&D that they prefer. So if someone wants to run an OD&D version of Birthright or a 4th edition version of Birthright or anything in between, I say goodluck to them.
