How VA chose to apply IOM and other statistics to agent orange exposure and vascular disease has never made much sense.
VA cedes that exposure to dioxin is connected to IHD (Ischemic Heart Disease...the equivalent of coronary artery disease) but not to other vascular diseases. Arterial vascular disease (atherosclerosis, hardening of the arteries) is a systemic disease of all arteries.
Although the disease may present in one bodily region (the heart, the legs, the arteries leading to the brain) it will be present in other parts of the body as well.
That in 2010 IHD became a service connected and agent orange presumptive condition at the direction of Secretary Shinseki surprised many. VA relied on the report: Veterans and Agent Orange: Update 2008 to make the ruling.
The claims made after the IHD nexus was approved caused huge delays and budget overruns at VA for years to follow.
Although the IOM 2012 report may have provided more evidence to support ischemic stroke to agent orange, there hasn't been any legislative activity to support that and VA won't be using that to adjudicate claims like yours.
The statements you obtained, "it is just as likely as not" isn't very effective. It is interpreted to mean that there is maybe a 50/50 chance that there is a service connection. The statement that usually prevails is, "It is more likely than not..." which indicates that there is a preponderance of expert opinion that favors the claimant.
I generally recommend that the veteran obtain an IMO (Independent Medical Opinion) from a civilian expert physician to appeal a claim like yours. Please click https://www.vawatchdog.org/imo-ime-medical-opinions-exams.html
The civilian IMO physician is probably going to use recent data to support that it is more likely than not that the ischemic stroke was caused or contributed to by agent orange exposure. The civilian IMO expert's opinion is very hard for VA to refute.
Finally...VA never uses the benefit of the doubt rule. While the rule is there, it isn't a hard science as to when or how it should be used.
If forced to answer whether or not you were given the benefit of the doubt in this decision, I'm confident VA would say that you were. They would argue that you were given every opportunity to prove your alleged service connection and that you failed to do so. It's a matter of semantics and perspective, and we never rely on VA to give the benefit of the doubt.
Your best hope is an appeal guided by a veterans law attorney along with an IMO.