I would pick a motherboard and go from there. I like the SiS 471 for VLB-based boards. It is fast and has a datasheet so there is a lot of knowledge about how it works. The UMC 498 is a good VLB chipset as well. Others might like the OPTi 895 or other chipsets.
Any VLB board is compatible with the 486DX2-66 and will be able to take maximum advantage of it. 33 MHz bus operation is trouble-free, too.
Some VLB boards were built without a 3.3V voltage regulator. This means 486DX4 and 5x86 CPUs will require an interposer to operate. That adds cost and might lead you to a 486DX2-66.
Older VLB chipsets do not support operating the CPU's internal cache in write-back mode, so 486DX4, 5x86, and Pentium OverDrive CPUs won't operate fully as they were designed when run in those boards. They will drop to write-through mode for compatibility. This has a minor but measurable performance impact. Some otherwise-good, later VLB boards may not be correctly wired for such operation even when the chipset supports it, and would require modification to do so.
There were at least some boards like Packard Bells where the Pentium OverDrive and external cache can't be used together. So you would watch out for compatibility issues if you choose that CPU. I think an Am5x86 (or Cyrix if you want to go that route) 486 system and a separate Socket 7 Pentium system makes more sense.