Hello!
A couple questions I would have would be: Have you made an Express before? Is this project an alternate "take" on something you've already done? If this is your first plunge into the Express world may I suggest you build a pretty straight-up version (Like the Kelly '90/Francesca schem) and then change it from there. You may be surprised at how cool it is!
Also... How much of a tweaker are you? Your plan will provide for many options, like SS vs. tube rectifier, etc...though you may find, like I have, that the original intent behind certain component inclusions was the right one.
For instance, I installed a choke as it was the better choice between it and the oddball 1K 25W resistor I had. I have since purchased a "proper" resistor, and I like what it does better than the choke, so out went the choke.
I toyed with the idea of tube rectification, but the SS rectifier has so much to do with the sound of an Express that I didn't want to alter that part of the mojo. The corresponding stiff power supply has a lot to do with the feel of the amp, and running a tube rectifier will necessitate less initial filtering that will "soften" the amp's feel.
So what I'm getting at is this. How much of a "real" Express do you want your Express to be? Deviations as you're planning will constitute all the ingredients of a great amp, but it won't necessarily be an Express.
Actually, I had all the same intentions you are proposing. My other 2 amps are tube-rectified, "choked", low-gain amps that have an amazing feel and are just an absolute joy to play. I figured I would install the same kinds of things in my Express build. Once I started the work I realized I didn't know anything about what an Express really is! So I shelved those ideas in favor of staying true to a Francesca-style build. I couldn't believe how much I loved it! It's by far my favorite amp now.
This may not truly answer your question about pitfalls to look out for, but I thought I'd throw in my $.02. HTH!
Shermock