As someone who has worked out and built several similar guitars with the same goal in mind for a few people locally, as well as a couple of non-specific Mooncasters (and modded a lot of Starcasters; really popular around here), I think there's quite a lot you will need to take into consideration if you attempt to make a Mooncaster match a Dot in tone:
1) Was the guitar you played the 335 Dot Reissue or just a 335 Dot? They look similar—the only difference on the outside is the Reissue's knobs are all-black while the regular model has black & silver knobs—but their sounds are quite different.
The Reissue is a discontinued model by the Gibson Custom Shop and uses a pair of Gibson Custombuckers, which are based on the Gibson Burstbucker but use AlNiCo III magnets and more mismatched coils. It uses the Custom Shop's Historic Reissue specification custom taper 300k volume and 500k tone pots with bumblebee capacitors. The centre block is also a little larger and the neck is a tiny bit thicker (on average; Custom Shop necks are profiled by hand, so there is some variation) and rounder. Of course it also possesses higher-quality cuts of wood.
The regular production model (not marked 'Reissue') is of course made in the regular Gibson factory. Compared to the Custom Shop version, its centre block is very slightly smaller, its neck is a tiny bit slimmer on average, and it's made with more standard cuts of wood (it's still a Gibson, so it's not like the wood is poor, but y'know, don't expect anything super-lightweight) and it uses more common 500k standard log & linear pots for volume and tone, with normal orange drop capacitors. Most critically it uses Gibson's standard 57 Classic and 57 Classic Plus humbuckers, which use AlNiCo II magnets and matched coils; both are wound hotter than the Custombuckers.
Overall, the Reissue tends to produce more extreme treble and bass than the regular production model, which gives the impression of its natural EQ either being 'flat' or 'scooped' depending on your taste and how you interpret having more high- and low-end. Conversely you can say the production model has a more mids-focused tone, which some people might perceive to be 'balanced' (since we're used to hearing mids-heavy archtops) but others may call 'soft' or 'muddy'. Of course these descriptions can change further depending on the set up of the guitar (especially pickup height and string gauge/material), amp used, and playing style, but as a general starting point, Dot Reissues have a more even and more dynamic response than most archtops while the production model is your more standard jazzbox sound.
2) Mooncaster/Starcaster guitars use a bolt-on neck, obviously, and this can significantly brighten the tone of the guitar's neck pickup compared to an otherwise-similar spec with a set neck. In my experience this makes more of a difference than the scale length does (i.e. even when using a 24.75" conversion neck, the bolt-ons are always brighter at the neck). So even if you make every other part of the guitar match, you need to over-compensate for the added brightness and use warmer electronics at the neck in order to make the neck pickup tone match that of the set neck guitars.
3) Warmoth's Mooncaster is a fraction smaller than a Fender Starcaster, which itself has less wood mass than either of the Gibson 335 Dots. Warmoth also does not offer a lamination design which is comparable to the maple/poplar/maple of the Dot, though plain maple will be fairly close. Overall, always expect the Mooncaster to be a little brighter and naturally have less bass resonance than the Dots.
4) Wamoth's 'Pro' construction is extremely different, in tone-altering ways, to the construction of the necks on Dots. So to match the sound really well you need to either grab a Vintage Modern or Vintage construction Warmoth neck, which restricts you to 25.5" scale (not that significant a factor in tone in my experience, as long as you compensate by taking some treble away elsewhere) or you need to get a 24.75" conversion neck from another company which makes them with more traditional construction. Of course the most important thing is that the neck feels good in your hand and you can play it comfortably, so ultimately you should buy a neck which fits your hands best. But just know that with Warmoth, at least as far as matching the Gibson's tone goes, you'll need to do some additional compensation to get around the construction and/or scale length.
Now, all that said, my advice for getting as close as reasonably possible to the Reissue's tone is to go for:
- All-maple body construction. If you order online then that means getting something with a flame, quilt, or birdseye veneer. If those don't float your boat, you could try an all-walnut body instead, since maple and walnut are fairly indistinguishable in tone, or Warmoth might do you a top of just plain maple if you e-mail them. (I can't vouch for this; a few years ago they did a plain maple top for a Thinline tele for me when their site wasn't offering plain maple, but it was a while ago and only they will be able to tell you if plain maple for a Mooncaster is an option today.)
- Mahogany & rosewood 24.75" or 25" conversion neck from somewhere else such as Musikraft or USACG. Sorry, Warmoth, but your necks are too different from Gibson's for the sounds to ever match. An all-rosewood neck can also work and is especially good at countering the normally brighter tone you get from bolt-on construction, or even 25.5" scale, though I can't say that it would be enough to counteract the Warmoth Pro truss rod. Do try to go for the thickest neck you can cope with without it getting in the way of your playing, because that extra wood mass really does make quite a tonal difference.
- Seymour Duncan Seth Lover or Gibson Burstbucker #1 neck humbucker. They both use AlNiCo II magnets but for the neck this is a good thing as it will help smooth out the bolt-on tone. (And once again, it can even help smooth out the tone of 25.5" scale if that's what you go for.) The Seth Lover will be a better fit if you've gone for a slightly thicker-toned construction (e.g. a walnut body or a thicker neck) while the Burstbucker will fit better with a guitar which has a slightly brighter-toned construction (e.g. a thin neck). If you're feeling fancy you could replace the AlNiCo II magnet with a III; none of these pickups are wax potted anyway so switching magnets in them is very easy, non-destructive, and mess-free. Switching from AlNiCo II to III will mean you lose a tiny bit of treble and overall output but retain the same bass, giving the impression of a thicker and more resonant tone. You could also use a 250k pot instead of the 300k volume pot that Gibson use, just to be sure the pot is knocking off that extra bit of treble that the Mooncaster's neck position has.
- Gibson Burstbucker #2 for a brighter-toned construction or DiMarzio PAF Master Bridge for a warmer-toned construction. The main difference is the Gibson uses an AlNiCo II magnet, so a little warmer than the Dot's, and the DiMarzio uses an AlNiCo IV, which is a bit brighter and more aggressive than the Dot's. Again you could swap in an AlNiCo III magnet into either of them to more closely match the Dot's Custombuckers, but the Mooncaster will likely benefit from keeping to either II or IV magnets depending on how you choose to spec out the body and neck. I would recommend you stick to the Gibson 300k & 500k values for volume and tone since the bridge pickup shouldn't need as much 'compensation' as the neck pickup, especially if you intend to mostly use the bridge with distortion.
For both bridge and neck, I wouldn't bother with any kind of super-premium boutique pickup because there's really nothing special going on here other than AlNiCo III magnets not being as common as II, IV, and V magnets. There's no special pixie dust which can be sprinkled on boutique pickups to make them sound more Dot-like; it's a super-simple wind and the Seth Lover, Burstbucker, and PAF Master already nail it. (In fact the Burstbucker #1 is literally the same wind.)
- If the guitar you're trying to match is a production Dot, not the Custom Shop Reissue, then just grab the Gibson 57 Classic and 57 Classic Plus pickups and compensate for the body & neck by using 250k volume pots to smooth off the high-end, or use Seymour Duncan Alnico II Pros which inherently have a little more bass and a little less treble than the Gibson pickups, which will especially help at the neck. Once again you could replace the magnets with AlNiCo IIIs in order to keep the low-end the same but drop the rest of the output and mellow out the high-end, to compensate for the body & neck.
