I have a newly installed & unmodified 1.0.1, I'll give it a shot shortly.
maniacbug I think did a great job putting the core files together, and making a couple of board types so there are options:https://github.com/maniacbug/mighty-1284p#readmehttp://maniacbug.wordpress.com/2011/11/27/arduino-on-atmega1284p-4/
I don't have any comment on the Arduino as ISP process. I had a dedicated programmer for '328s, the one from mdfly.com, that I used for a while.
After I got my system hosed with mixed up download speeds between bootloaders & IDE, I just stuck with using Atmel's AVR Studio 5.1 & an AVR ISP MKii for the bootloader, initially so I could easily check on the fuses & lockbits, and also because it was faters, and FTDI Basic for sketches. More recently I got some forum help getting around the default Jungo driver for the MKii so that the IDE could be used for bootloading, and now I just do that as the IDE comes up way faster than Studio 5.
There's the work WestfW to make a standalone bootloaderhttps://github.com/WestfW/
and that NickGammon expanded on with more description including updating to cover the larger chipshttp://www.gammon.com.au/forum/?id=11635
and went even farther with loading sketches from SD cardhttp://www.gammon.com.au/forum/?id=11638
I don't know if I can add significantly to all that, I'll see what I can do tho.
I do know I have a working bootloader that installs first time and sketches go in first time too.
Can't confirm it covers really large sketches, I've never gone that big, I've generally just needed dual serial and more IO pins without the necessity of adding shift registers to get there.