I tend to favor the A3640 but I'm biased since my A3640 now gives a WarpEngine a good run for the money. (Some extra memory would be nice though).
Even if you get close on ram speed(which motherboard ram is still slow),your still missing the nice warpengine scsi and the 64 or 128MB capability.. its way faster than the 4k motherboard ide. it can get close to 10MB/s.
The warp engine is way better than any 3640,overclocked or not.
the pals/gals on the 3640 run so hot they can near burn you lol. i imagine at 40mhz they are nice and warm(are yours heatsinked?). Also the cut the jumper/delay line hack delays access to ram if memory serves(pun intended) and you are still always accessing motherboard ram with delays,unlike the warpengine with proper ram.
Not to mention most all the 3640's rev 3 and 3.1(and some 3.2's are STILL wrong) need capacitors soldered correctly,some are usually backwards.i've fixed many that caps have leaked on and have eaten traces.
Is your 040 chip a 33 or 40mhz part? (sorry to hijackthis thread).
Like heiroglyph said,its a great upgrade if its cheap though, sure beats 030/25
as far as 040's go,the warp engine is one of the best,most reliable boards around.
mech