Again, by the time you even remotely stabilize or can take an accurate reading you're well over 1000 feet.
For now, the best thing to do is guesstimate and mention that there can be errors near sea level. Although if you do every 1000 feet up to 5000, it takes a little more writing down but can give you a better realistic estimate of sea level.
I did some climb testing before and I'd just have the E6B up and a pre-written table on paper, ready for me to just glance at the E6b the second my altimeter touches "1000", "2000," 3000," etc... and I'd write down the value and watch that altimeter again.
Then if you have 1,2,3,4K and you know the lower ones are off, you can kind of predict how the climb rate would extrapolate.
For example, here's a chart I did that way:

You can see how 1k and 2k don't match up, but if you draw a line from the others you can extrapolate where it would realistically end up.