With the lower bellhousing inspection cover off, you should be able to tell if the pressure plate and clutch are working or not. Seems to me if 2nd and 3rd shift fine, then the clutch probably isn't the issue. Could be that the input shaft is binding up in the pilot bushing causing the input shaft to turn enough rpm's to prevent you from engaging the gears (because of no synchro). Too high of an idle speed may contribute to this.
The only other thing I can think of would be there is an internal problem with the first/reverse slider gear. Pull off the side cover and take a look.
How were these parts stored while it was apart?
