Sorry I totally forgot to come back on this.
After making a flight and you want to alter the cruise altitude of that specific plan; go to the Flight Generation page, press the Edit Plan button, click OK on the departure runway, click OK on the Destination runway, type over the altitude value near the top of the route, example:
Cruise Altitude: 5000
to
Cruise Altitude: 9000
Also you can edit the waypoints or delete some as you wish.
After that click OK and the route will rebuild the same but according to your new altitude value and link up the new waypoints. It's really intended for only minor alterations.
For making plans along specific waypoints of my choosing I would use a manual planner like PFPX to alter the IF10 route as it is or maybe create a complete custom route from scratch, then output as a plan type that IF10 can read, the flight can be regenerated loading that custom plan or dropping it on IF10 to initiate loading and building that plan.
Regarding places the profile has visited: On the main map page, look at the row of small buttons at the top right corner. 'Show routes' places lines between each pair of locations you traveled. Maybe showing perhaps simply the location dots on the map and providing a text based record might be helpful - i'll have a think about it, Thanks for the suggestion.