It's hard to beat drawboring, you can drawbore ahead of time rather than during fitting by moving the tenon peg layout.... If you're determined not to drawbore, I'd think that drilling all the way through mortise and tenon would be a way to go. The challenge in that process is to have the drill bit coming out in the right spot on the opposite side of the timber. This wouldn't matter on outside joinery, only where you can see both ends of the peg.
For handsaws, I like the Zeta saws(although 11inches is big for these blades), available from tashiro's hardware(prompt processing on orders) -timber blade and king rip blade.
http://www.tashirohardware.com/ You could also check your local sharpening person, they will often have a rip saw or two hanging around(literally) and for sale.
I've always plumbed and braced as I go, it takes about the same amount of time to place a bent plumb as it does to place a bent crooked. Also, if you don't plumb as you go, your plate braces will be a nightmare. In my opinion, saving pegging for later just means more work to do later.
