I have a small tank that is need of some planting reorganization maintanance etc. It will not be a huge job, but will involve the removal of most of the plants - consisting of mostly bolbitis and java fern on driftwood.

In short, what are the best ways to reduce the stress on the fish while this is going on and in the hours following? Or am I worrying too much?

If your fish are otherwise healthy don't worry about it.

My fish like harrassing my hands (or my siphon) when I do maintenance, and they also associate me being anywhere near the tank with food, so in general they don't seem to mind me being in there working. The exception is my pleco which is a grumpy old hermit and hates everything.

One thing I do want to mention is that you will probably pull up alot of mulm and possibly some pockets of nasty gas in the substrate. This can be harmful to fish so when I have to rip up plants I keep a siphon going in the tank and have it hovering at the base of the plant while I pull it up so it can catch anything nasty coming up out of the substrate.

Agreed. Healthy fish, that are used to human interaction don't seem to be bothered by maintenance.