It seems most people modify their bikes at least the ones who check into forums do so this advice may be helpful
Decide on how much you want to modify the bike and save money on not chucking extras which cost real money
For instance, if you intend to replace the exhaust, don't buy a model with the Termi.
If you do like spoke wheels, they are probably cheaper buying the classic or Urban Enduro than aftermarket
The 62 is a little cheaper but apparently a lot lower performance. The flat tracker seems to be a cosmetic upgrade you should only buy if you like the looks
Then comes looks, what resonates with you? Fenders, colors etc. Easy to change tank side panels and handlebars so don't worry about them.
So think about what look you want or maybe you want to save money for better suspension components or exhaust. If you want a comfortable seat, you'll just have to have the OEM reworked or buy a custom one. Your arse will let you know if you need it.
Look at some of the bikes others have built. 'find a look you like and then do the economic analysis to build it most cost effectively.
Personally I really like the Classic but put lower and narrower bars plus a Dart fairing. Makes longer street rides nicer but on dirt roads it isn't as comfortable standing up.