What are you using for an amp currently to rule your Yamaha receiver is more transparent than the Line-2? I can't imagine any receiver especially a $250 AVR has a better preamp section. Not sure if you're cranking the treble on the AVR giving it more brightness it seems to sound better or what is going on.
You mentioned you replaced the tubes; did you do them all and do you have any means to check them. I have an older Arcam AVR and it's ok and my father has a much newer higher priced Marantz AVR, but it's no where near his Line-1 in performance and your Line-2 should be even better. Maybe that Yamaha is just a giant killer?
I bet the 508.24 still holds its own. I wouldn't rule it out as not being a nice performer with all the gear you are discussing. If you are running some 25 year old cables I'd invest the money there first, or if they are new but the entry level of whatever brand, you should experiment with proper cables. This gear should sound really good with nice cables.
The 508.24 was a well regarded player. Sure newer players have improved and maybe an Oppo 105d makes sense if you're system is mixed into a home theatre set up as well. Agree you might be better spending money on your source than your preamp, but I wouldn't get in any hurry.
Hopefully you have a tube tester or have a shop locally that can test your tubes and put the Line-2 on the bench to check it out. Something just doesn't sounds right if you're preferring your Yamaha. If you have your Line-2 plugged into some A/V power conditioner with your A/V equipment trying plugging it directly into the receptacle; same will be true with the Pass you have coming.
Best of luck