Bike Forums - Upgrade or replace broken shifter (and maybe drivetrain)?

Yesterday, the cover on my right shifter/brake lever combo broke off while coming home. The plastic at one of the screws had broken off a long time back - now the other one came off. Normally, this would be a $5 replacement, but the shifters (Shimano EF-29) are old (stock from 2002 Trek 4500 MTB) and the cover has apparently been discontinued. Shifter still works fine, but I doubt it will for much longer given how much rain we get here. Since I can't just replace the cover, I'll need to replace at least the shifter.

I have three options from my research:

The EF-65 (Acera line) is the new version of my old shifter. It looks like I can get a pair for ~$30.
I can upgrade to the Alivio line with either a combo shift/brake or separate units (something like the M410). This is probably $40-60 for just the right shifter.
I can upgrade to something like the Deore line, but this will require replacing the chain, rear derailleur, and cassette since 9 speed will not work with 8 speed (at least, not well).

Cassette and chain are 6 months old and the RD works fine. I will need to replace the cranks soon, primarily because they and the bottom bracket are worn out and the stock FD on the bike does not shift well (many reports of this). I have no reason to upgrade to 9 speeds, but do shift a lot since my whole commute is a series of hills, so nice shifters would be nice.

So:

Is it worth it to have separate brake and shift levers?
Is it worth it to pay 2-3 times the price to go from EF-65 to M-410? Will I notice any difference? This is the only bike I've ridden extensively, so have no experience with higher end components.
Is it worth it to replace the whole drive train to upgrade to the Deore (or better) series?

I don't mind spending the money, but don't want to just waste it.

Thanks for any help.