I'm no expert, and the schematic would help, but:
The not being able to set D0 and D3 sounds to me like a dodgy DIP switch. Did you check that that was working?
Is R/W being connected to +5v at the DIP switch? That would cause problems like you describe. It might also damage the CPU.
What I would do looks something like this:
Code:
-------------+ +------------+ +5v
65C02 R/W |-----------|>o--+--|/OE1 | |
| +--|/OE2 | +---------+ |
D0 |-------------------|O0 I0|--+-------| DIP |---+
D1 |-------------------|O1 I1|--)--+----| Switch |---+
| | | | | +---------+
| | | | +-[3.3K]-+
| | | | |
| | 74xx244 | +----[3.3K]-+
| | | |
| | | GND
This thing: -|>o- is a not gate.
I've only shown two data lines to make it clearer, but you'd do the same for all the data lines.
I hope you'll be able to get your board working.
I'm going to go a different way with mine(stacking boards), but that's the beauty of this hobby: near-endless variety.
EDIT: You may also have to take Phase 2(the system clock) into account. I think the 'C02s accesses are valid when Phase 2 is high. Someone else will be able to confirm that. You'd run Phase 2 and R/W into a NAND gate instead of just R/W into a NOT.