I'm really liking this map so far!
I've got one annoying bug and a few comments about missing resources.
The bug is in the trading system. For things like certus quartz, where you get 4 quartz as the result of the trade, if you trade for enough of it at a time you don't get all of it... the turtle's slot 1 empties out and the turtle.dropDown(items) doesn't drop as many items as it should. (It's possible that this could be a problem with 1-item-result trades too; I'm not sure.) At the least, you should check before the turtle.dropDown() and wait for it to have enough items; or to allow the trading to proceed more quickly, you could switch to other slots and drop the items from whatever slot has enough items in it.
There's another minor issue with the trading system... if you want to trade for a lot of tin at once, you'll have to have iron and tin in the chest/pouch at the same time, so you'll end up accidentally trading for some ferrous ingots. Maybe you could adjust the ferrous ingot recipe? For instance, adding a cobblestone as an ingredient would make sure you didn't accidentally trigger the trade. (I just go into the trading dimension and terminate the ferrous-ingot turtle's program whenever I want to trade for tin.)
And a couple of missing resources. I was going to wait on Forestry farms until I did some bee breeding to get apatite (I've got some MFR and Steve's Carts farms instead), but then I noticed that the apatine bee is bred from a rural bee, so we can't get it at all. (Plus, I like the "gotta get them all" idea of having one of each possible serum vial.) Also, some of the bee products are "specialties" that only show up if the bee is in its preferred temperature/humidity biome. Maybe at some point you could give access to a mystcraft tiny-biomes void age with a nice variety of biomes for bee breeding and production? (I think I'll make one myself, relaxing the rule on making mystcraft ages to allow it as long as it's a void age.)
The other missing resource is mystcraft crystal -- I'd like to make some portals, but I can't. (I'll probably make another mystcraft age just to get some crystal, and not get any other resources from that age. I wonder if crystals show up if you make a void age that includes the crystal symbol? Probably not.) How about adding a recipe for crystal? I'd suggest one diamond plus a stack of end stone gives you a stack of crystal.
Edited to add: I forgot one more missing resource. Evidently Magic Bees added some new hives? I think that the Infernal bee (that you need to breed the Tinker's Construct bees) comes from a hive that we don't have access to. Not sure if there are any other missing hives/bees...