That evap is already drilled for top feed bottom return. I would have drilled the return hole on the opposite side. That would force more refrigerant to flow through and around the lower level. Just keep the return hole at 12 o'clock(up) then. Hopefully that will allow some flooding down below the return.
Yes, just clean the surfaces that will be brazed for now, the acid will get the rest afterwards. Having a flat evap is crucial for lowest cpu core temps. You will need to lap the evap after brazing. You won't be able to do a good job with the flexline attached so you should braze a 3/8" x 3" stub for now. You can't acid clean with the captube brazed in so you'll need to drill the captube hole to 3/16" and braze in a 3/16" x 1" stub. Then you can slip the captube inside the stub for easy brazing.
You should leak check the evap after you braze it. Crimp the end of the 3/8" stub shut and braze. Slip a 1/4" schrader valve over the very end (just 1/8") of the 3/16" stub and braze. Leak check at 150psi. If no leaks then unsweat access valve, cut 3/8" stub down(1 1/2") and proceed with acid cleaning then lapping.
That compressor has POE oil so make sure you keep it sealed until your ready to braze and pull vacuum.
What type of flexline are you using?
Sure.. post more pics.