Hi, Berlinguyinca,
Not to gainsay the other posters, but if at all possible, build it stock. I'd suggest acquiring a new top plate, building it stock, and if you like it, build another kit on your flipped top plate after you have at least the stock build experience. Incorporating a mod into a first build is chancy at best - highly likely to result in problems and the risk of ending up with an incomplete project - and fairly stranded without support - is very high as well. Even having many builds under my belt, the first time I attempted this became the last time I attempted this, and this wasn't a flipped layout, which is an extreme mod.
I'd offer a comment about support. Bottlehead's support policy, both through their team and by offering and moderating this forum, is amazingly generous and highly effective. However, providing this high level of support for modified projects isn't scalable, and doing it for one means doing it for an unsustainable many. I don't believe I've ever purchased a product whose warranty would be honored had I modified it, and can't imagine why Bottlehead's products would be any different.
Having built mirror-imaged amps before, I can say that some parts of a layout and circuit just don't mirror, and it's not as straightforward as it seems to be at first blush. Yes; wire lengths will be different, but, mirrored or not, the pinout on tube sockets and other components will always be the same, so some connections will not look just like the mirror image of their stock counterparts. Even with this experience, when I built my pair of Bottlehead Paramounts, I considered, and quickly discarded, the notion of building mine as a mirror-imaged pair. The Bottlehead layouts have been carefully developed, optimized, and documented in the manual, and as I said, a great many components, if not most, just don't mirror. My time was, as is yours, limited, and I didn't want to risk a pair of unfinished paperweights sitting on my workbench.
If you're dead-set on attempting the flipped or mirrored version of your Crack, I'd suggest a hybrid approach, as opposed to attempting a full-on mirror. I think another poster may have been alluding to this as well; perhaps you meant this too, so I apologize if I've misunderstood your questions and am restating the obvious.
The core of the layout is on the center of the top plate, so it's the same when flipped. Keep that portion unaltered, and build as the manual instructs. Number all terminals around each component (use a sharpie marker on the bottom of the top plate) the same as the manual shows, even around the components which are in different locations. The headphone socket, the RCA jacks, the power entry module, the volume pot, the on/off switch will have to be connected to/from the same terminal numbers as in the manual, but the wire routings and lengths may be different in a lot of cases. Here, you're definitely on your own, and at risk of inducing hum and noise. I think at least one reason the parts are where they are is the Bottlehead team has made a layout that minimizes hum and noise; power and signal lines are keys to this, and you'll have to move them.
And, fwiw, I, too, have painted top plates on the wrong side before. Don't drink and paint! Even though I spent a fair amount of time on prep and paint, I got over it and got out the belt sander - an amazing productivity tool, btw (be sure to wear a mask and eye protection), and got on with it. Yes; there was a bit of a time penalty and delay to do this, but I'm sure that was saved many times over in a smooth and predictable build.
Hope this helps; whatever you do, good luck with your project.