I'd consider either Lucerne or Zurich.

Zurich - Munich : direct ECs every 2h, seat reservation recommended (3€ through tickets.oebb.at)

Thinking of maybe dropping bags at a hotel in either then getting a train south and back via Bern maybe - how much do you think could be done in a day?

Third option : hotel in Bern.

From there head to Interlaken and take a boat on either Lake Thun or Brienz (fully included with the pass !).

The next day : Bern - Lucerne -> RE train (more scenic than IR15) and then Lucerne - Zurich - Munich

OR

DAY 1 Colmar - Bern - Interlaken Ost - boat to Brienz - Lucerne

DAY 2 Lucerne - Zurich - Munich

Btw you can always drop bags in lockers at railway stations.

I’ve gone for Lucerne - hoping to do the Brienz train then boat to Interlaken - is it train then to Thun or is tere a boat option before returning to Lucern via Bern?

There's also a boat option !

- Brienz - Interlaken Ost boat

- Interlaken Ost - Interlaken West 5 min train or 20-25 min walk

- Interlaken West - Thun boat

You can also leave the boat in Spiez and walk 15-20 min up to the train station (would save 30 min on your way to Bern).

Schedule example :

- Brienz - Interlaken Ost 15:40 - 16:53 boat

- Interlaken Ost - Interlaken West 17:00 - 17:04 train

- Interlaken West - Thun 17:10 - 19:20 boat

It's perfectly doable, I've taken this route 2 weeks ago :)

From Thun you have multiple options to go to Lucerne :

- fast route : departure 19:34 (connection in Bern)

- more scenic route : departure 19:39 (connections in Konolfingen and Langnau)

And of course you can stop along the way wherever you'd like.

it might be better to get the train from Lucerne to Interlaken Ost then the boat to Thun as I would like to be back in Lucerne earlier than 9pm  is that achievable?

It is possible yep but I'd say that Lake Brienz has more beautiful scenery than Lake Thun. The journey is also a bit shorter so it'd allow enough time to walk a bit around Berm historic center :)

Something like that :

- Luzern - Brienz 13:06 - 14:33

- Brienz - Interlaken Ost 14:40 - 15:53 boat

- Interlaken Ost - Bern 16:00 - 16:52 (train every 30 min)

- break in Bern, you can walk to the terrace in front of the Federal Palace in a few minutes

- Bern - Lucerne : either 18:36 - 20:03 (scenic) or 19:00 - 20:01 (faster). Those trains run hourly

so Global pass include boat trips at Brienz / interlaken / Thun and the train ride from Colmar to interlaken? does it worth using one day of Global pass?

hi yes it is included, about if it is worth you might look for the high ticket prices in Switzerland. Without looking up would say it is worth using.