I had some similar issues with my recent game as the Confederates. I had a very successful 1st day where I was able to drive the Union troops off the high ground at Cemetery Hill and Culps Hill. I decided to choose the "Crush the Yankee's" scenario to prevent them from regrouping against me. When the battle began, I noticed I had gained Anderson's division from the 3rd Corps but I was missing all the brigades from Heth's division. This was irritating for me because I had held Pettigrew's brigade back to use as a sledgehammer to break the yanks.
The battle itself was incredibly fun, I was only reenforced by Hood's division from 1st Corps while the Union kept getting division's streaming in constantly. The battle seesawed back and forth around the wheatfield and devil's den for most of the morning then once I determined the union troops were exhausted, i made a heavy push up both Round Tops. At the same time I was pushing them off the hills, they made a heavy push against my center and left flank just south of Cemetery Hill and Culp's Hill. It was touch and go for awhile before I was able to get some stabilization to my lines but I managed to hold the hills and stopped the union push at the base of Cemetery Ridge.
So after that scenario, I am thinking I am in pretty good shape. I hold all the good ground and I still have McLaw's and Pickett's divisions yet to arrive (and maybe Heth's division will show back up?) while the Union is down to only VI Corps left as reenforcements. The rest of them are pretty chewed up with the exception of V Corps.
So I load the next battle up and I am only given one choice. It is a Union counterattack on Seminary Ridge! All my troops have been placed either on Seminary Ridge or north of Gettysburg in the open fields. I was a little frustrated so I stopped playing but I do intend to finish it since it should be a huge challenge to take back all that ground in the condition my army is in after that rough morning on the 2nd day.