It is not and never was Siamese.
The siamesing was part of the casting, not of an operation during the manufacturing process. It's hard to tell from the pictures (nice job using a mirror!), but the surfaces of the intake runners give me the impression that they have been sleeved (tubes inserted).
Drilling the plastic adapters may be an option, but I suggest you first investigate how you would attach hose barbs -- e.g., if you have enough meat in the plastic to use even a 1/8" NPT hose barb, and then enough clearance (to the next adapter) for attaching a hose.
BTW, I wonder how these plastic adapters were attached to the manifold. There doesn't seem to be space to get a socket or spanner over the nuts. Maybe the intake manifold was drilled through and bolts were used from the back instead of the original studs from the front? This would mean the intake manifold would have to come off for servicing the plastic adapters (which then also poses the question of how the plastic adapters were sealed towards the manifold, and whether or not such drill holes for bolts (or sleeves) affected any of the water passages -- which then may explain the water you found). If you can track down who made the conversion, it may be worthwhile talking to them.
All that being said, there are a number of 2600s that run without a brake booster (mostly because failed brake boosters have been bypassed). I was told it takes more force (but not an excessive amount) on the brake pedal. So, that may be an option to consider as well.
Last but not least, one can buy small 12V DC vacuum pumps on eBay for about $20-25 (see search here
) that maybe worth a try. If they produce sufficient vacuum quick enough, I have a hunch they could easily be hidden near the vacuum container in the engine compartment, and that would save you all the grief of dealing with the intake manifold and/or plastic adapters.