MakeCD surely can handle 350 MBs of data. I did the same thing - I burned a whole bunch of s/w that I d/led, though I wish I understood how to do it in multisession first, which I do now. I burned it directly without a buffer, but my CD burner is a Plextor PlexWriter 12/4/32 on my SCSI chain. I would venture to guess that either your HD and/or CD is not correctly set up on your IDE. BTW, I would leave your CD drive at PIO 4, as fast as it can go. I myself have the A1200 FastATA MK III from Elbox & this device definitely cuts down the amount of time it takes to burn CDs when the data is on one of the HDs connected to it. That's one of the big reasons I got it. I've got 2 2.5" HDs connected to it. The master drive is a Toshiba MK4006AV 4GB drive that I've had for years & is now the "Master", while I just added a 160GB (149GB usable) Seagate ST9160821A HD as the "Slave" drive in the chain. They're both capable of PIO5, although it appears that with the Elbox s/w-h/w combination, the fastest speed is currently PIO4. And this is all inside a standard A1200 casing.
I would first ask yourself if you yourself notice that your HD access is quicker on the whole. If not, check to see if it's set up correctly. If this is not the problem, then it must be the way your CD is set up. Did you also install the Allegro CDFS?