First of all, Welcome to the forum Mike. The LT is a wonderful machine even if she does have a few issues that can spoil a good day of riding.
The Brick engine is often called a box of rocks so some noises are OK while others indicate something needs attention.
If you have the time, money and inclination to do your own service, buy a Clymer manual for it as it is an indispensable resource.
I had the same thing with my rear brakes. Another issue is the cow bell effect when the rotor gets too lose which I didn't have. The grinding I never put a finger on but I went with the EBC rotor and all those issues disappeared, at least so far. pads are cheap but you can inspect them and the old rotor and make a decision if you want to try and reuse them. I would just spend the $20 or $30 bucks and put new pads on a new rotor but save the old ones for when you need them. Just be wary that they will, new or old, ed to bed in and your breaking will be reduced until they start making good contact.
The final drive is a toss up. 2003 was in the time frame when failures of the crown bearing were more prevalent and there are other issues that need looking at if you are in there. Your mileage and year are right about where many had failed but then again, many have not failed also. Checking for play is good and turning it by hand engine off listening for noise might reveal something or not. It would depend on what state it was in if it was actually failing. Dave ( Saddleman ) is the resident expert and re-builder extraordinaire of the FD's If you have any concern, send him a private message and inquire about his services. Dave is in NC also so maybe not that far away. I did my own but then again, I also went and bought a spare in case I didn't get it right. There is a bunch to know and some special tools so it isn't just a R&R of the crown bearing. If they go, they usually do so quickly once they start. The magnet is a good place to start but if the oil was just changed as you said, you may not get any indication there but if you do, now would be the time to have it fixed.
Front tire cupping is an issue on the LT with lower air pressures or the balance of the tire or both. Increasing the pressure some will help but a cupped tire will remain cupped. Up to you on how much it affects the bike and if you want to replace it before the tread is worn. Be aware that your rear tire options are limited as spec is a 79V rated tire with reinforced sidewalls. She is a beast and that limits you to only a few mfg. Front has a few more options with a 58V spec.
There are a few things to look for on your bike. One is does it still have the original rubber break lines. If so, they are an accident waiting to happen. They deteriorate from the inside and can burst at any time likely when you need them most. Spiegler makes a stainless braided set for the LT and they are the lines of choice for most unless you want to try and have some made from the old ones.
The 2003 has the I-ABS brake system with servo assist. There are known issues with these system module failing and they are an expensive ticket and no one rebuilds them yet. Keeping the system regularly bleed can help but won't necessarily prevent a failure. New lines will help keep the fluid clean and bits from clogging up the controller module too. Procedures are documented on this site and also in the Clymer manual.
Watch ALL of Kirk's videos on the LT from the Illinois BMW motorrad club. Another valuable resource if you are turning your own wrenches or to learn about this wonderful bike.
Illinois BMW Riders - Maint./ Repair Videos
Welcome and good luck with it.
Gordon from Sugar Hill, GA