1) Breed in Maximum fertility. If you already have the extra bees machine, you can just use a serum. But the point is to have that 4x drones when you attempt to mutate.
The reason is simple, the chance to mutate is _per_bee_.
2) Nocturnal is the absolute best trait for speeding up everything
3) The second best, unless you're in a no-rain biome, is flyer. However, there is _absolutely_no_ base forestry bee with the flyer trait and you have to look to one of the expansions to get that trait.
4) The tropical/exotic/edenic line is the only base forestry bees to produce combs that create honey 100% of the time. Imperial bees outproduce only if you're willing to squeeze honeydew.
5) Save honeydew, it has a lot of great uses.
6) Setup a cloning system to turn all of your excess bees into exact copies of each other. When you're done mutating a breed, and have all the serums you want, throw that princess back in the cloning vats. When you want to mutate a new breed, take a princess and drone that have been fully cloned and apply the breed serum for the two breeds needed for the mutation
7) Until late in the Thaumic bee lines, the best effect for these cloned bees is Explorer. Free xp for no risk and no server load. If you've got 6-8 bees running at the same time, the xp is very fast. (There was a bug that still gave xp even after the queen died off, that's fixed, but simple automation can keep the same effect)
8) The acclimatiser can get you BOTH_5 tolerances for both humidity and temperature. These tolerances are passed on to offspring and can be captured in a serum. Use water and lava to get UP_1 in both categories, then when you switch to sand and ice they will convert to BOTH_1 and stay at both all the way to 5. (Note, anything more than BOTH_3 for humidity is wasted)
9) Alvearies Alvearies Alvearies. That's where your honey should be going. Even with three frames, apiaries are slower. Without those three frames, the apiary isn't worth the effort. Since frames cannot be automated (which is intentional, and not a bug, and will not be changed) it's a lot of manual effort. Your first alveary is an imperial, your second an industrious. Your third a Cultivated. Why the Cultivated? Because the first two don't make beewax.