I have AndyF's Toyota alternator conversion on my car. It has been running good for a couple of years. In the last few days, my voltage is sometimes low on startup and won't increase until I increase rpm over about 5,000. At that point, it jumps from 12.6 to 13.7. I have driven the car at the 12.6 rate for several miles and the voltage doesn't drop as I would expect if it wasn't charging (wife in car and she gets nervous when I get on it). It doesn't do it at every startup, but it is starting to get more frequent. I have a volt meter in the car and the Sniper handheld shows the same voltage. They both get voltage from the starter relay. The battery is fully charged as I keep it on a battery minder. I have checked for voltage drop and haven't found any obvious bad connections.
This has me baffeled.
Other than swapping out the alt, does anyone have any suggestions?

The current from all battery come out of the negative post of the battery and retunrs to the positive post so checking the grounds (negative leads, you can't have too many good grounds ) would be the first thing I would check, corrosion occurs

I would first check all connections both pos and neg. at all main connection points including the battery, block, starter etc. Make sure the cables are in good condition
Next, You might have the battery tested as they have been doing some strange things the last few years.
if accessible you might check the output at the alternator stud. ground to the alt case, and then the battery
Otherwise likely alternator have it tested