I had a Gran Rally. Great all-around bike. Sold it because I had too many bikes. I changed to an 8 speed rear cassette instead of the stock 6 speed freewheel. Original rims were unusable when I got the bike.

Looking over you list, I'd recommend adding the fenders and rack. Good changes for a commuter. Get a set of Koolstop pads. Stock brakes will probably be just fine. Ride the bike for a few months, then honestly evaluate what would be an improvement. Changing parts just for the sake of change is fun, but gets expensive fast.

I'm currently riding a Univega Gran Turismo. Originally I was going to change to a 9 speed set up with bar-end shifters. The cost just didn't make sense. When I find a decent set of 700c rims for cheap (severe budget issues) I'll replace the 27" 6 speed ex-Peugeot rims ($25.00 on C-list) and go to an 8 speed cassette using the original friction shifters. After riding the bike for about 1,000 miles, friction shifting works fine for me. Did get a Brooks B-17 because the stock seat was missing. Worth the price. $80.00 from Nashbar.

I had the Gran Turismo powder coated because the stock paint was gone. $115.00. The GT is a keeper. Might now just go with a rattlecan job just because pretty bikes are more attractive to thieves.

*edit*

saw your first post in re Gran Rally. Changing to a 10 speed set-up means new chain, front chainwheels as well as the the other stuff. 8 speed stuff works well with friction shifting and the stock chainwheels. Might have to replace the chain. Can't remember if I did or not.