A TY won't count as a PGY-1 in IM. You will get credit for any month that you do exactly the same thing an IM resident would do in the same program. Most TY's include some surgical rotations, sometimes some peds, etc, and none of that will count. Basically, you'll probably have to start again at the PGY-1 level. You are correct that you'll only have 2 months of your TY done by then, but perhaps that will help.
However, if you want neuro, you best bet is to look for an offcycle PGY-2. Some people who matched this cycle will drop out -- either their visa will have a problem, they will have an illness / family emergency, they will change their minds, fail out of their PGY-1, etc. Those spots don't go into the match, you simply have to find one. That's what you probably want to focus on. If the program you're going to has a neuro program, then you want to contact the neuro PD. Chances are, if a spot opens up he/she would hear about it. The only bad news is that your TY might not count fully as a prelim year for neuro. There are very specific requirements for what can and cannot be in a neuro prelim year -- you might want to review that before you choose what rotations / electives you get. If your TY doesn't fully meet the requirements, then you start your Neuro residency in July, and then somewhere along the line (or at the end) you make up a few IM blocks. By then, the neuro PD should be able to talk to the IM PD about getting you 2-3 months of rotations to complete your training.