Crikey, where to start? Oh, that's what you are asking
Starting with published routes:
There's the Capital Trail which loops through the various hills south of Edinburgh. Very steady as a three day trip, a bit more challenging over two.
The Wild About Argyll trail. The full route is pretty long but it twists and turns so much that it's quite simple to shorten it according to your needs.
The Highland Trail. I'd choose the southern loop rather than the central one, generally much more rideable (but there's still some H-a-B) and you can do part of the central loop to extend it - head up from Fort Augustus to Cannich then short cut back into Glen Affric to pick up the return.
The Cairngorm Loop is pretty tough, mainly the inner loop, so stick with the outer loop and avoid the "sting in the tail" going out to Fealar Lodge.
Other loops.
There's lots to go at (surprise) but here's a few that I can think of at the moment.
Ben Alder tour. Two options:
1. Dalwhinnie - Loch Garry - Loch Rannoch - HT550 route past Ben Alder to Culra bothy then back to Dalwhinnie
viewtopic.php?f=10&t=9015#p106320
2. Dalwhinnie - Loch Garry - Loch Rannoch - Rannoch station - Corrour - Laggan - Ardverikie - Loch Pattack - Dalwhinnie
viewtopic.php?p=289897#p289897 (this trip took a "short cut" along Loch Ericht - read it to see if you fancy it)
The Moray Triangle. Not done this, looks generally low level and gravel bike friendly
A route we did last year - Cannich - HT550 route to Contin - through Strathconon to Craig - pick up the HT550 return at Achnashellach - Dornie - Glen Licht - Glen Affric and back to Cannich.
viewtopic.php?p=273016#p273016
Have a look through the Trips and Reports sub-forum, I've posted about the two Ben Alder options and the Cannich route. There's also stuff on my blog -
http://bobwightman.blogspot.com/ Fatbikephil has also posted lots of suitable routes, he's also a blog
http://philsbikepacking.blogspot.co.uk/ with lots of reports.