That's a great bike and sounds like it's set up beautifully! I owned a '94 and have owned three other XR's (XR600, XR400, XR250) and XL600's.
Al Baker died many years ago. When he ran XR's Only himself years ago it had a great rep, he built a lot of Baja racers from XR600's. The new guys (maybe family?) that took over had some problems early on. Now? I'm not really sure. Hopefully they are doing good work ... you'll find out soon enough I guess!
What caused the Top End to fail?
Could be your bike was run low on oil? (XR-L's don't like that) ... or perhaps bumped off the rev limiter one too many times? They DO run hot. Quality synthetic oil is a must, IMO.
The Valve job and high comp. piston should be a very nice improvement. Jetting the XR-L is tricky. If your guy got it right then kudos to him.
Only "possible" down side with High comp. piston might be that you will need to run higher octane fuel. Pinging is a characteristic of the XR motor on low Octane gas. So if you go to Mexico (where I ruined a top end on crap barrel gas) then try to get the good stuff, which is now nearly everywhere in Mexico, even Baja.
The CDI box is odd, should not have failed. No idea on this. Honda electrics are normally very good. Very expensive part, should never fail again.
Super Trapp is OK if not too loud, this, with jetting and air box really wake the bike up. Good stuff. Lower gearing is great off road and around town but you may want to go back to stock sprocket for any longer road rides. (easy to change front sprocket)
Lowering links are great if you're too short for the bike. It is VERY tall in stock form. If you are tall perhaps put it back to stock height, especially if you want to do serious off road. If not, leave it low, it will actually handle better on the street in lowered form. I like the heavier Eibach springs.
The Corbin and IMS are excellent, as is the Scott's damper. The Scott's is a $500 extra alone! Man, this bike has it all! Somebody knew what they were doing and weren't afraid to spend money. Pro Moto Billet rack? Shoei helmet? aRE you kidding? All excellent stuff.
The XR-L will last pretty well if you take care of it. Keep valves adjusted,
Do a plug check to make certain its not running too lean. (HOT!) keep
fresh synthetic oil, clean air filter (watch that K&N, it does NOT filter out dirt worth a shit ... I prefer a Twin-Air) If doing street only, then K&N is fine.
What sort of riding do you intend to do?
Weak areas of XR650L:
1. Runs a bit hot
2. Can use a bit of oil if run hard ... critical to keep level UP to FULL.
(learn how to check it correctly ... must be HOT to get accurate reading)
3. Rear sub frame and battery box are weak and will bend if overloaded.
Need to be reinforced for RTW travel. Do not overload.
Strong areas on XR-L:
1. Very good go anywhere off road dual sport. Strong and reliable.
2. Good basic suspension, strong motor, reasonable weight.
3. Mostly good build quality, will last well if cared for.
4. Good handler off road.
That's about it.
Go to Thumper Talk Honda XR forum to learn a ton about this bike from other owners. They are mostly dirt riders, not travelers.