1) Tiagra vs Sora - Tiagra pushes me to the top end of my budget but is it worth it over saving a bit of money with Sora? Also, I discovered today that Tiagra/Sora isn't just limited to the groupset, so if it's not full Tiagra, e.g. if the brakes are Sora, is that going to make any difference? I'm assuming it's the groupset that will be the main thing.
The problem with being undecided and making a compromise you are not totally happy with, you will end up upgrading which will cost more than getting the better specs the first time. The most important components are the shifters and the rear mech which you will use a lot and have a much higher impact on the overall experience. The others are unlikely to make a noticeable difference at this level so you can save on those if you want.
2) Allez vs Secture - Is there much of a difference? They said people go for the Allez even for commuting etc and in general they didn't give the impression that I should go for the Secture. Then I though, that while I could ride the two for a test ride, they may feel fine for 10 minutes, but build up to a few hours and that's a whole different ball game. What they did say was that a proper fitting would help so could an Allez with a proper fitting be better than a Secture with a bad fit?
Allez has a sportier frame, Secteur has a more comfortable geometry, the rest is design and colours.