If and when you pull the intake to look at the lifters don't remove any of the push tubes. Just maybe you didn't get this push tibe seated back in the lifter. I don't think you said it was like this untill you removed it and tried to reinstall it. But really, you need to pull the intake and valley pan to look at all the lifters. Sorry but thats what things look like from my place in all of this. Heres hoping the cam is ok. Don't remove the injection pump tower or you will be working on that timing problem thats for sure. You can pull the intake and valley pan without the tower coming off easily. Pictures are always good so all of us can be there with you and add more help. Plenty of us have been down that road too. I always take digital pictures of what I do. Sometimes I forget what I did internally and refer to my pics just to feel better about what I have done. It sure beats taking things apart because I forgot what the timing marks were set at or did I install all the bolts or oil cooling jets....