540ci is a lot for any a833, even an 18 spline.

Maybe their concern was more about the choice of trans and less about the modifications.

With the torque a 540 produces it's likely 3rd gear is going to be nonexistent given enough traction. You'll shear the teeth off 3rd gear speed gear and cluster gear before you break the modified parts.

A $1000. quote sounds like it includes disassembly and reassembly. The website quotes $120 per gear (3x$120=$360) to faceplace or Pro Ring and then the cost of two modified sliders. I would expect $600-$700 without the additional labor to build.
Some options: Jerico 4 or 5 speed, G-force 4 or 5 speed (I have a Long H-pattern shifter for the 4-speed for sale), Tremec TKX, Liberty Extreme-T, Passon, or maybe something from a Vipor T-56 with upgrades, etc.