Hi Sven,
now I have time to give you an answer ...
With Routeconverter you could do a lot of your work: you can load your single tracks and save it as one track. You can load your track and run through it point by point (it will be fast) to search for mistakes and jump backs ...
You could load and convert your shoreline into a lot of formats.
Routeconverter is freeware. If you have problems to see a background map, try the 32 bit version instead of the 64 bit version and vice versa.
http://www.routeconverter.de/home/en