I have a different set-up, but similar in ways...

Yamaha RM1X drum machine/midi sequencer
Access Virus Indigo 2 Synth
PC running Live

So, hardware and software, similar in that respect... this seems to work for me -

RM1X midi out > Virus midi in.
Virus midi out > RM1X midi in.
Virus midi thru > PC midi in.

I program everything on the hardware, as i suspect you do, then Live picks up the midi clock signal (sync mode set to midi clock) and the EXT button is activated...
Set this up so live is synced.
(you press start on your hardware and Live kicks off. It will be badly synced till you go into pref, while your hardware plays a simple 4/4 kick and have Live play a simple 4/4 [say, closed hat] on every beat, then adjust the sync delay while it plays back till its proper synced [mine is set to -24ms])
Now Live is synced to your gear and this means if you have a line running into your PC from your mixer, you can for instance, start the 909 and Juno (live will now kick off too of course) but have just the sends from the Juno channel running into a new audio channel on Live, hit record on the Live channel - there goes that loop into Live, then start a fresh sound with the Juno while still playing back the recorded loop and 909.... and just keep layering your sounds as you create them and your hardware can always be in the mix and it will all be in sync with the audio running on Live...

Eventually you will have enough audio in Live to compose your finished track, then when you have plenty of songs finished just cut them up and throw them all into a new Live set, and still be able to jam all your original hardware patterns over the top...

I dunno, this method seems to be sweet with me at the mo...

You mentioned some kind of unstableness with Live, check you are running the ASIO drivers if you have them , I think they are the best.. Although you were saying about midi notes being dropped and all - this method just uses Live as a synced sampler, dealing with just audio - not using the midi editor, but you can also use it if you have extra midi ins.

Hope this might be some help

;)