Hi Swat,
This is useful Topic for checking out potential problems :
What to look for when Buying a Pre-Owned ( Used ) Trophy SERegarding the specific issues mentioned :
You can tell if it's been lowered by looking at the bottom of the Rear Suspension Unit
to see if the drop Links have been changed.
The stock Drop Links are approximately 131mm between centres :

To LOWER the bike, LONGER Drop Links are fitted !
The front Forks may also have been raised in their clamps slightly ( around 10-12mm or so )
which will be noticeable in the upper clamps. Prior to lowering the top nuts are flush with the upper clamp :

I believe that Top boxes are still available to buy New from Triumph Dealers,
along with the various coloured Lids to match your Trophy.
It is the same Top Box as used on the Sprint GT.
You will have more difficulty finding the Sliding Carriage that the Top Box mounts onto,
and may have to look at "pre-owned" items being offered for sale.
Another consideration here is that all new Trophy motorcycles had a spare Lock Barrel,
keyed the same as the other locks on the bike, for use if a Top Box was purchased,
as new Top Boxes are supplied without a Lock.
Check if the Trophy you are thinking of buying has the spare Lock barrel - sometimes it will be found
stored in the Tool Roll under the pillion seat, or in the under seat storage box, or the glove box.
If buying a pre-owned Top Box check if it is provided with a Lock and Key.
The locks can be extremely difficult / fiddly to remove for replacement without causing damage
and you may have to settle for having a different key for the Top Box !
Some Members have fitted other Top Boxes such as Givi to their Trophy.
I'm not personally aware of any 100,000 mile Trophies, but I'm sure there are some !
The Final Drive / Rear Bevel box do not seem to suffer the same failures that you mention.
There have been a few where Oil seals have failed requiring replacement of the Seals,
but very few reports on the Forum relating to failures of the complete drive.
There have also been a handful of total engine failures - usually attributed to a failure in the
Camshaft drive, either the Timing Chain breaking, or losing tension and slipping teeth
resulting in valves hitting pistons.
There was an early "Upgrade" that was NOT classified as a "Recall", where a modified Cylinder Head
was fitted free of charge to Trophies up to VIN Number 602960.
You should check if the Trophy you are interested in has had this work done if it is below that VIN Number.
While there is no direct information to suggest that any engine that did not get the modified may fail,
I personally wouldn't buy a Trophy that hadn't had the work done.
I can't advise on the asking Price / values, as it's all relative to how many other similar Bikes
are on the market in the area at the time, the Sellers Profit margins, and how keen they are
to move it on, so have a search on Craigslist etc for some comparisons that you can use to barter with.
Cheers

