Shameless plug: I've been doing lots of modelling cycling for transport, and realized that it's hard to get accurate height data for either a road or a GPS trace. I've since solved this problem, if it's of use to you... https://github.com/fiftysevendegreesofrad/BayesianDrape

Good luck with the project - I like the focus on MTB especially since Strava deleted all the interesting downhill segments (which was a loss to us all) and also with Trailforks going the subscription route.