You didn't mention what brand/model of OT.
Assuming yours is comparable to theirs (which is in doubt because we don't know what they used), coupling cap type can have a subtle effect on the overall sound. Assuming your amp sounded "98% like theirs" if you used polyester caps and they used polypropylene, their amp might sound a little brighter.
If it is a difference you can't adjust for by turning the tone control a hair higher, you might look into swapping the caps. Or you might drop cathode bypass caps a bit (to 1-5uF) to shave bass and leave the amp a little brighter overall.
You might even have preamp tubes which are a little fuller than what someone else used. Swapping the input preamp tube will make the most impact out of any of them.
Then again, even the old amps sound a little different between samples. I doubt Mark Baier modified a whole lot in the circuit; at one time 20 years ago he was pretty obsessive about trying to get every little part optimized (by selecting different component types, finding the perfect tube sample for each position), but I'd bet he can't do much of that anymore in a manufacturing environment. Unless you're unhappy with your amp's sound, I might let it be what it is. And if you want to change it, you can do anything you'd like.
I have a home-built 5E3 copy, and it sounds like a Deluxe to me; I've never given it a second thought about whether it sounds identical to someone else's copy. It doesn't sound quite as luscious as the '55 Tremolux I once had, but that amp had a bigger cabinet and a 50-year old speaker, so the comparison might not be realistic.