Hello E39 swapper, from a former (recovered) E39 swapper. I did an LQ4/T56 into an '01 540i Sport almost a decade ago.
The smartest thing you have done yet is ditch the bare block. You'll spend as much time finding the parts for/building the motor, as you will performing the rest of the swap.
I recommend carefully examining your budget and goals before continuing. These aren't particularly difficult cars to swap, just some extra coding/wiring in the cluster to keep the tach, CEL etc happy. Where it starts to get tricky is the ancillaries. Your car looks to be a 6 cyl model - therefore open diff? Your clutch dumping shenanigans will result in a one tire fire that will get old fast. Now you're into building an M5 LSD that has its own tax, or swapping in an IRS 8.8 pumpkin (lots of fab time).
The 6 cyl subframe also uses rack and pinion steering (better than the 540i's recirculating ball) which will allow you to use the more readily available rear-sump pans. The swap mounts can be built yourself, and the geometry is significantly easier if you start with a 6 cyl chassis.
Looks like you'll want to enjoy this as a daily driver - what's the plan for AC? You'll need custom lines to mate the GM compressor to the BMW condenser/evap, as well as figure out a way to trigger the GM PCM to turn on the compressor (either manually switched, or by modifying the IHKA).
Transmission? Depends on your power goals. T56 = $$, and honestly doesn't shift all that great, even with a rebuild. The other options are CD009 (350Z trans) w/ adapter, or the tried and true autos (4L80E) which are dirt cheap and work. They're a lot less boring than you might think.
Then there's the usual LS swap stuff like:
-What harness are you using? DBW or DBC? Buying a premade one or thinning out a junkyard harness?
-How are you tuning the car? Buying HPTuners and tackling that learning curve or taking it somewhere for a dyno tune?
-What are emissions requirements in your state? In NYS I had to deal with passing a plug-in OBD2 check (can be skirted with some creative HPT work).
If I were to do it all over again, I'd skip the big lumpy cam and the T56 and go right for a 4L80E/turbo. WIth the right converter it'll be fun off the line and even a 4.8 with a sloppy turbo will make 500whp by accident. By some happy accident the cheapest combo (4.8/5.3 turbo w/ 4L80E) also makes for the fastest car.
I'm subscribing to your thread, let me know if you have any questions.