Problems with GVP 68040/33 64mb ram

[Oldsmobile_Mike]

Did it work correctly before? How long since you last used it? When you say the hard drive is "slow", what are you basing that in comparison to?  What version Workbench?
 
In general you want to use the SCSI controller on the accelerator, but the controller on the GeForce '040 is notoriously slow compared to the controller on their HC8+ series, for example. Roughly half the speed. But it does have faster transfer to memory than a controller in one of the ZII slots. Pick your poison, LOL.

[Oldsmobile_Mike]

I would start by checking your startup sequence for any tools that might conflict with the 3.9 soft-kicked ROM's. Here's my thoughts: since 3.9 (especially if you have all four of the Boing Bags) replaces so much of the ROM's anyway you can run into conflicts, it's best to not attempt to remap the actual ROM image into RAM. Just let 3.9 do it's thing and you'll be fine.
 
You should also check your jumpers, guides should be available on BBOAH or the amiga.resource.cx page. Also measure your hard drive speed with SysInfo - that's an easy baseline, what speed is it reporting?
 
3.9 is going to be slower at window redraws because of it's multi-color icons and the ECS chipset. I assume you're using something like high-res laced 16 color mode? You can mitigate this somewhat by installing PFS file system and the Peter K icon library.

[Oldsmobile_Mike]

No prob, man. I would recommend a clean install followed by all four Boing Bags, in order. Only compatibility issues I've seen with PFS are with some old programs that don't support drives larger than a certain size, can run into problems copying files onto them. That's why I recommend keeping your Workbench partition to around 400MB, and keep it within the first 2GB of space on the drive. Oh, don't try using DiskSalv on any PFS partitions, either.
 
Using SysInfo 4.0 I get 24.31 MIPS, 6.18 MFLOPS, 22394 Dhrystones. That can vary a little bit, SysInfo isn't the most exact program but it's good for baseline tests. I've got a lot of hacks and patches installed to improve performance, but some of them can slow it down a bit too, LOL.  
 
With an 8GB 600x CF card hooked up as my primary hard drive I get between 1,700KB-1,750KB read speeds in SysInfo. This is the peak limit on my controller per Ralph Babel's chart. Disappointing, since the HC8+ can theoretically do up to 3.58MB/sec. I tried for a long time to run a GeForce '040 simultaneously with a HC8+ but kept running into memory corruption issues, never could get that sorted.