Try repurposing your periodic boosters to a second clump of them where you lose momentum instead?
Fair warning: You will probably run into chunk loading issues.
On a tekkit server where I acted as world architect a while back I built a transit network using high speed rails (rails blocked off, machinery at each end to provide/remove carts, etc)... it was a lot of fun to build.
The system worked great until the server ran into even a small amount of lag. The high speed rails are faster than op flying... so the server has to race to keep up with the chunks. If you happen to hit a chunk that isn't loaded right and there is a desync your cart pops off of the track.
After everything was said and done it turned out to be more reliable to build Multiverse portals to move people from "station" to station. In FTB I'd recommend using Mystcraft portals to accomplish the same. With Mystcraft you could even build the train infrastrcuture and then 1-2 chunks out from the "station" have it go through a mystcraft portal to instantly warp 1-2 chunks out from the destination.