Given my whole newbie-ness to sysex and BCL, I am not exactly a wealth of info. And because of the probability that you wont see this, I will be v brief at this point, so:-
1. I do not believe you mentioned turning off bulk protect. I believe this is necessary, at least for sysex.
2. The A3000 will respond to CC's for many parameters, though these are not visually updated on the A3000 display. I am yet to discern the exact consequences of this.
3. I have been using the bzone editor, and A3000 Remote (A3000rmt) to 'capture' the sysex commands. Along with some virtual midi loopback and midi ox, I have been able to run the A3000, BC Manager, and the A3000 software all at once, so I can see the sysex in Midi ox, and copy it to BC Manager via the BCL editor, then send to the BCR and test. Seems to work well, though I only got my first encoder working yesterday after a day of effort. Mostly the delay was down to midi configuration to get it all working together (I dont know why as when it finally clicked it was quite simple).
4. Whilst I am hoping that, having got one encoder working, the rest will be easier, there is some difference in the sysex for other commands, in that 'emulating' the front panel encoders only requires one commands (albeit with a 'reloffs' variable), wheras other sysex requires a parameter selection to be sent along with - and prior to - the parameter control sysex. As yet, I dont know how tricky this will be.
IF (big if) you, or anyone else does read this, I apologise if I have used any incorrect terminology, and hope not to have 'added' to any confusion.
Whilst I harp on about the lack of anyone reading this, given the well known issues with the encoders on the A series samplers, the BCR makes is a great solution, particularly if you have other uses for it. It is, of course, a rather expensive solution for the sampler alone, but even then, given the nature of the sampler, it works really well as a 'synth', so having the real time control offered for all the parameters, and not having to lean over to your rack and go through menus almost makes it worth suggesting that an "a-series + bcr" combo, could well be a reasonable purchase proposition as a synth for someone that owns neither. (Well, that is what I am hoping for anyway, and the signs are good so far).
A Little off topic, but honestly, in the many synth reviews I have read over the years, many have complained about the lack of onboard control. Those that have gone on to have a tarnished reputation as a result could all be considered in any synth shortlist as a bargain purchase as the BCR will obviously remove this shortfall. I guess this is likely true of any controller, but I am really v v impressed with the BCR's potential. I am a little embarrassed that I am saying this so late in the history of this unit, though when I was researching controllers, so few (if any) of the newer ones were as flexible as the BCR, and most seem to focus on CC's, with little or no sysex support.