Well thanks for all the replies.
I decided to have another go, my PCMCIA Card adaptor on the PC is starting to play up now, but so far this is what I've managed.
I installed Fat95 from Aminet.net and also cfd along with the compactflash.device file.
Was simple enough but the problem I was having as I've had previously was that when the card was inserted the Amiga would freeze for ages. Any activity would be unuseably slow.
It worked fine on ClassicWB install that I had previously though, but the strange thing was that ClassicWB doesn't use CF0 file in the DOSDrivers folder to mount the drive, so I was a bit confused at that.
I overwritten the Amigas compactflash.device file that came from aminet with the ClassicWB comactflash.device and now it all works perfectly.
I've also created a copy of the WB disk with these files so when I boot from it, I immediately have access to the PCMCIA CF Card. This way I can copy the files from that disk onto the hard disk ready for when I install Workbench again. It means I don't have to open up my Amiga and put the internal CF Card into my PC Card reader.
As for Dopus, I think I'm gonna just dump the copy of Dopus from ClassicWB with the config files onto my fresh install of WB then examine the Config file to see what other files I need to copy across to make it work.
That will just leave WHDLoad to install.
Once I've done that I'll install any other programs as and when I see the need.
With regards to the CF Card size, I didn't know you could use anything over a 4GB, but to be honest, I don't really want to spend any more money on CF Cards, instead I've just removed all the CD32 games and CDTV games from the drive and made plenty of room. As far as I've seen, there's no diference in most of them anyway other than BASS which has speech and I have kept.
I should also be able to fit all my demos on there now too. So I think I'll be happy with the 4GB CF drive.
It's only to play old classic games, and maybe I'll get it online one day so I can download files from Aminet direct.
I'm not even sure if I'll bother with OS3.9 either, since I don't really know of any differences that would benefit me. I'll maybe just install some of these icon packs I've seen.
Thanks again for all your help.