Man, haven't been inside my v5 in YEARS!
About the tray not ejecting: Weren't there IR micro switches or something for detecting the tray retracted/extended state? It's a long shot, but there could be something wrong there. I've seen them cause wierd tray issues with PC drives before. Might be worth checking out. Either that, or the signal from the eject button is not making it to the chip to kick off the eject sequence that would spin down the drive. (or the chip(s) on the board/modchip/wiring could be bad).
As for the drive spinning at power up....that is an odd one. I'd have to go with the bad chip scenario. It may be failing the initial disk check on boot up, which could be a number of things. I've seen PC CD drives fail because of bad firmware/chips. If you've got a v5 board, you could eliminate the "Sony" chips as a culprit--pain in the @$$ to do it, but at least you could rule the system out as the culprit and concentrate on issues with the drive hardware or modchip.
Hell, if the board and mod check out OK, it might be easer to just drop a new drive in there and see if it behaves.
If it ain't broke don't try to fix it! But, hell if you can tweak that bastard just a little bit more....hehehe.