Hand made pasta with wholemeal flour
I make partially wholemeal-flour pasta, and have tried 100% wholemeal also; I prefer the former. 

Let's start with the dough. I think a couple things are at work:


wholemeal flour will take a bit longer to hydrate than refined (e.g., all-purpose) flour;
wholemeal flour will generally absorb (require) more water to fully hydrate than AP flour.


I'd suggest the following:


After mixing just until incorporated (still perhapas a bit ragged) allow the dough a period of rest (wrapped in clingfilm/plastic-wrap) on the bench, for perhaps 15-30min, before the major kneading phase. It will allow the dough to hydrate and relax a bit more. With this rest, you can probably get away with closer to 5min of kneeding (phew!). Compare this SA question and this Fresh Loaf for a discussion about bread dough and resting.
If it's still dense, consider a further teaspoon/5mL or two of water per egg. Note, though, that this water is best mixed when you're first mixing the egg and flour (it's more messy and difficult (albeit possible) to add later). Large eggs are perhaps 50mL per egg so keep that in mind -- too much hydration will make things hard to work with.


As for the cooking: are you drying the pasta first, or are you putting it straight into the water?  I find wholemeal pasta takes perhaps 50% longer to get to the cooked'ness that I seek (but not more than 4-5 mins in rapidly boiling water), but certainly not as long as commercial pasta (10+ mins).