Ok, after doing some more testing, I have a bit of an update on issue 2.

After detecting that there is no bootable cd in the drive, it'll query the floppy, and just sit there with the floppy light on searching for a disk. If I reboot with a disk in the drive, it boots up just fine from the floppy. Am I missing something here?

UPDATE:
So, I swapped the drive boot order in the bios; CD -> C -> A. It hit the CD, didn't find a bootable disc, moved to the C drive and BAM, invalid system disk.

The last change I made was using the DOS SB installer.

So, my path with this version of the rig was: Partition hard drive; C,D,E,F. Install DOS to C. Install 95 to D, install VIA, Video, Audio (vortex) drivers. Swapped out vortex for the SB16. F4 boot to original OS (booted without issue). Installed SB16 DOS installers, CTCM, etc. Reboot. Lockup.

Did the SB changes screw up the boot files?

I'm thinking I should start from scratch. Install DOS, Install SB16 stuff. Install win95 then VIA and Video drivers and see where we go from there.

About the vortex issue: You can disable the gameport and prevent win95 from detecting it:
- copy the vortex2 drivers to your harddisk
- edit the file AU30MMED.INF
- search for a section called "AspenOverides.AddReg"
- uncomment the line "HKR,Config,DisableJoystick,1,1"
- save, remove all traces of the original vortex2 driver in the Windows directory (Don't forget C:\WINDOWS\INF)
- let win95 redetect the Vortex and point it to the modified driver

I have no specific idea about your HD problem, but I too had some issues when installing DOS and win95 on the same harddisk if both OSs had a primary partitiion for themselves.
Some random thoughts:
What geometry translation did you select in BIOS (CHS, LBA)? Does the BIOS have an option to disable DMA or UltraDMA harddisk access? Maybe the boot failures are speed/DMA related.

For the second problem :

Looks like the boot flag is missing. Dos and Win9x's FDISK can't set a non-primary partition as active. Boot with a DOS 6.22 boot disk. Check the contents of the "C:" drive. If it's the DOS partition, try entering "SYS C:", provided SYS.EXE file is in the boot disk, to transfer the system files to the C: drive. On which partition is your Win95 installed?

Or,

Try this:

1. Use a 3rd party partition manager to create 2 PRIMARY partitions. (Delete all partitions first and start from scratch.)

- MS-DOs's partition manager won't allow you to create 2 primary partitions on the same drive.

2. Reserve the first part of the partition with 8GB for DOS, at the beginning of the drive.

- here, you can do one of two methods :

i. Only reserve the first 8GB space and create the parttions after installing Win95, or,
ii. Create partitions for DOS in the 8GB space, and then "HIDE" the partitions using the partition manager.

This is to make way to install Windows 95 first.

3. Create the rest of the space to create a FAT32 partition, provided you're installing a FAT32-supported version of Windows95.

Install Windows 95.

4. After installing Windows 95, and after completing all reboots and making sure Win95 is working well, now either

i.-Create the partitions for DOS in the first segement of the reserved space, or
ii.-Unhide all partitions.

When creating the DOS partitions, continue as you have made before, i.e. - 1st partition is primary and the rest are created in extended logical partitions.

If you're planning to hide and unhide, you can even use DOS' FDISK to create the partitions first, hide all partitions with a 3rd party partitioner and use the Win95's FDISK to create another Primary Partition with the FAT32 format. The hidden partitions will be shown as Non-Dos and FDISK will permit to create a primary partition.

After completing Windows 95 installation and all the reboots, you can then unhide the DOS partitions.

Once this is done, you can use the FDISK in either program, to "SET ACTIVE PARTITION", to boot into either partition. When in DOS, and you would like to boot into Win95, use the FDISK in DOS and vice versa in Win95.

By using a FAT32 partition for Win95, the DOS utilities like defrag and chkdsk won't mess up with the Win95 files, since the DOS 6.22 can't "see" a FAT32 partition.

Finally, you can try using Boot Managers if you don't want to mess with partitions. e.g. - Smart Boot Manager, PLOP boot manager.