When considering swapping a master cylinder from a 2004 Chevy 5.3 to a 1999 GMC 5.3, there are several factors to take into account:

1. **Compatibility**: The master cylinders from different model years, even within the same brand like Chevrolet and GMC, might have variations due to updates in design, brake line fittings, reservoir shapes, or mounting points. These small changes can make a significant difference in whether or not the part will fit and function correctly.

2. **Brake System Design**: The brake systems in vehicles are carefully engineered to work with specific master cylinders. Using a master cylinder that is not designed for your vehicle could lead to improper brake function, which can be extremely dangerous.

3. **Brake Line Fittings and Thread Pitch**: Ensure that the brake line fittings and thread pitch on the master cylinder match those on your vehicle. Mismatched fittings can lead to leaks or difficulty in achieving a proper seal.

4. **Mounting Location and Bolt Pattern**: Check if the mounting holes and bolt pattern align perfectly. Even if they are off by a small margin, it can cause issues with installation and stability.

5. **Brake System Electronics (if applicable)**: If either vehicle uses additional electronic components in the brake system (like ABS), make sure the master cylinder is compatible with the electronic systems. Sensors or connections might be different across model years.

6. **Booster Compatibility**: The compatibility between the master cylinder and the brake booster should also be checked. Different master cylinders could have different depths where they meet the brake booster, which might affect pedal feel and brake pressure.

Given these potential differences, it's generally recommended to use a master cylinder that is specifically listed as compatible with your vehicle's make, model, and year. If you insist on using the part from the 2004 Chevy 5.3, here are the steps you should take:

- Compare part numbers and specifications of the master cylinders for both vehicles.
- Physically inspect both master cylinders side by side to check for any obvious differences.
- Check with auto parts suppliers or use online compatibility tools to see if cross-references exist.
- Consider the possibility of having to modify fittings or other components, but remember that modifications could compromise safety.

If any doubt remains, it is safest to procure the correct part specifically designed for your 1999 GMC 5.3.