the use of metal alignment dwells ( 25mm brass pattern maker dwells ) and the use of coach bolts WITH WASHERS is a safe bet.
I also use a strip of 2" x 1" framing timber as a shelf at one end about 2/3rds the length of the baseboard width ie L shaped. By doing this the assembled board can be aligned and clamped up prior to drilling the hole for the pattern makers dowell. The male / pointy dowell end will also be protected by this shelf.
To ensure consistency you could make up an end jig ( mark BOTH faces ) so the drilled holes will be consistent for each end.
An alternative to the coach bolts is to use door hinges , one on top and one on the bottom of the ends to ensure alignment, then use the hinge pins to hold it all together .
Another suggestion , though I am well aware that it is considered overkill, is to use cork tiles from Bunnings attached to the top of the ply baseboard. DO NOT glue, but use double sided carpet tape to attach the cork tiles to the baseboard top. This allows you to remove and replace at a future date if you wish. The double sided tape will hold, after all it is intended for carpet tiles that you walk on .
The cork top will allow you to pin the track formation to the baseboard while you line everything up , and you can then glue the final alignment to the cork if you wish. For this I would use carpet laying PVA , as this is flexible and can be lifted with a spatula. ( Get a spatula for your own use, it is NOT a good idea to use the kitchen food spatula ) The carpet PVA should be decanted onto a smaller application bottle with a small nozzle, the $2- shops will have something suitable.
The decanted portion is then thinned by approximately 50% and a drop of liquid dishwasher detergent added to lessen the liquid's surface tension. You can then dribble the liquid over the sleepers between the rails, you only need a small amount as capillary action with take it under the sleepers , you can also use a cheap artists flat brush ($2- shop again ) to spread it if your dribbles are too much. let it dry for a minimum of 24 hours . ( Keep the watered down PVA separate from the main supply, do NOT pour it into your main PVA supply as the contamination will cause the whole bottle to go of. PVA does have a shelf life, so store in a cool dark place. )
You should also consider using graphite grey black closed cell foam sheets to form your track base.Woodland Scenics and TrackRite Australia sell this stuff in pre cut rolls, I personally think the TrackRite Australia is preferred as it is designed for Australian conditions, and industrially is used in expansion gaps in masonry and road works. You can also get this from Bunnings in BIG rolls ( who may also sell it by the metre, ask them ! ) , or in thin sheet from from Clarke Rubber, who sell it by the metre.
The thinned carpet PVA will stick the closed cell foam to the cork, and also the track base to the closed cell foam. In both cases it can be lifted and reused if desired. I suggest the closed cell foam as it is a sound deadener, and it gives a small amount of movement to assist with expansion and contraction , which will occur with a wood baseboard , and anyway the real track does also move ! You do not need to use a lot of PVA , a little will go a long way , and despite initial appearances , a small amount will do the job.
( I am NOT a fan of glueing track base to hard surfaces as inevitably the track formation will buckle due to heat expansion , and you get a continuous rumble sound which becomes really annoying. )
For your consideration,
Best wishes and regards, Radioman