That bandsaw fence, I think is really nice.
Might you adapt the bolt holes to be slots instead, so you only need to loosen the bolts slightly and lift the "Track" off to use the mitre sled? My old SIP is very secondhand: at some point in its life someone did that to its rail (I think because you have to remove its rail to change blades). There is, or should be, relatively little pressure on the fence, so the rail doesn't have a lot of force on it, so slots (with washers) shouldn't be a nuisance. Failing that, might you simply cut a slot in the angle to take the mitre sled's bar? I doubt it would have much effect on the fence arrangements. Although it would weaken the angle a bit, that probably doesn't matter much.
Personally I wouldn't countersink the bolts (if I understood your post on this, you're intend to countersink the bolts on the angle/rail), as it removes the ease of adjustment, if you need it. Slots + washers would be a lot better for this. If you find there is a fence setting where they get in the way (there almost certainly will be), consider just using a piece of straight board as an auxiliary fence so that you don't have to lock it in the 'nuisance' position.
Regarding tracking, etc. You do need to do this with every blade change, but it becomes a quick routine. If you're starting with the wheels in good order (tyres, bearings, etc.), and coplanar with each other (in line), and at right angles to the mitre slot, then it should be fairly easy to get it to track accurately. You can correct for drift - Steve Maskery has an excellent bandsaw DVD which I learned from - but if it's set up right you can eliminate drift for all practical purposes.
I feel your pain regarding that mitre fence - mine on an Elektra Beckum was similarly bent, although not as bad. It's a very similar design too, and I think part of the problem is that the castings are machined before the metal has "settled", and/or the machining operations allow the metal to get too hot. I still haven't fixed mine completely, but I vastly improved it with a big hammer! I can't split it, because there aren't enough mountings to hold each side independently (and your setup must now be horrid!).
Nice work though!
E.