The Amaranth is best automated with a golem that has a USE core and have it plant the sapling. Use MFR for the rest of the farm. As for the forestry stained glass, yea that was painful. No way to automate it at all. I tried every side for imputing items and nothing worked.
I was going to try golems, but couldn't be bothered to go through the crafting stages, and, will you look at that, I've got that stock of activators from where I dismantled my sifting and shard rigs. I also set one up with three, one to plant, one to apply the hoe of growth, and one to apply the axe of the stream. Cost the axe, but eventually got through it all.
I have to say, I'm starting to struggle with a willingness to carry on, the rewards are becoming more and more like tokens, rather than something that'll actually help (as tends to happen in a sufficiently advanced minecraft game). I need to get the staves researched (damn instrumentum), the last section of bees, get the remaining dirt, and wait for things to finish crafting (damn, compressed cobble takes a while), but I know that I'm unlikely to get much that's actually going to do anything, so I'm a little hesitant.