Hi Mike,
The exhaust guide is still the same length it was when Honda made it, and the top of it is in exactly the same position it was in when Honda assembled it. All you've done is put it back the way it should be.
It is quite usual for valve guides to extend into ports. This is necessary for two reasons. The first is to get the largest possible bearing area for the valve stem, so it will take as long as possible for the guide to wear out. The second reason is that the hot gas in the combustion chamber heats the valve head, and this heat has to be conveyed to the cylinder head. The main heat transfer path is through the valve guide.
In the case of the exhaust valve there is another reason as well. The hot exhaust gas flowing through the port past the valve heats its stem even more than the combustion process heats its head. Hence it is particularly important to maximise the amount of the stem that is in contact with the valve guide. Protecting part of the exhaust valve stem from heat by taking the heat directly into the valve guide, improves heat transfer efficiency because tranferring heat from the valve to the valve guide is not very efficient: there is clearance between the two, so putting the valve guide in the way of the exhaust gas, is much more effective. Of course there are limits: you don't want to obstruct the exhaust port more than necessary, or maximum power will be reduced, and the valve is made of far more heat-resistant material than the valve guide is, so you have to be careful not to overheat the guide.
You'll find that valve guides - even the ones that are integral parts of the cylinder head - normally extend some distance into the ports, just as yours does.
