I would go to an aircraft structural maintenance guy, these are the guys who are qualified to sign off repairs to primary structure, and have them devise a repair for you. They don't do a lot of calcs, they just use established practices from AC43.13. He might not want to sign anything, because it is a homebuilt, but if you find the right guy, he will show you a beefup you can do and you can show the DAR that you have addressed the issue.
But the first thing i would do is calculate the cross sectional area of that member at the location where there are the largest holes called for in the plans, then calculate it with at a location with one of the holes you drilled and and see what the difference in cross sectional area is. It might be that you have not reduced the minimum cross sectional area at all so maybe you can convince the DAR to let it go.
I think the critical design load in that member is tension, when you do a max G pull up. The down force on the engine/prop will be something around 1500 lbs at 6G, assuming a 250 lb engine (Wt numbers pulled from a hat) so the engine mount would pull down like crazy on that longeron. So the stress on that member is the tension load divided by the area. This is oversimplified, because the member is riveted to some sturdy skin, but you get the idea. IF you have swiss cheezed that member too much then it won't be as strong. But increasing the hole size by a bit might in certain locations not make much difference. On my RV4 I have a row of #8 holes along there that hold on the top cover, by design. And I have an O320, same engine as you probably so same loads. And there are some -3 AN bolts in the top of that angle where the longerons attach to the flange where the engine mount loads go through, so there is quite a bit of area reduction there.
Frankly I don't see this as a problem. The issue is convincing a DAR of that. DARs are generally A&Ps, not engineers and they won't want to stick their neck out, which is understandable.
Homebuilding is all about solving 100 problems at a time, as you know. This is another one, but there is a way forward.