big George

Hi guys,
I bought an ebay 92-95 civic DX tranny for my 93 SI. I replaced the original because I had a binding in the shift linkage that was getting progressivly tighter, with minor grinding in second, third and reverse, and a clunk heard & felt when I engaged the clutch. The original SI tranny is an S20-Y4B. The one I received is a DX S20 Y4F. I installed the Y4F. The SHIFT lever is again hard to move through the gears (same problem I had with the Y4B) It takes considerable effort to shift and WORST OF ALL the NEW tranny is Grinding in second and forth and not engaging at all... although first , third, fifth and reverse seem to engage and put power to the wheels. I first thought it was the shift lever actuater not traveling far enough due to rust binding it up..used penertrating oils and lube... no better...
Also, The metal face of the old clutch plate was warped and worn on one side with metal shaved off the face and a spring was also shaved down. (I now suspect this was the cause of the clunk heard and felt and maybe explains the grinding, but dosn't explain the binding of the throw.)
Installed a new OEM clutch pack and had the flywheel turned although it appeared perfect.
So, is it possible a DX has a slightly longer shift rod? or is there an adjustment I can do to lengthen the throw about an eigth inch. What about the Binding of the shift lever?....I live in the boonies 65miles from the nearest Honda Stealer...Don't know where to find a tranny rebuilder.
I hope you have suggestions other than telling me that I'm a sucker and should have gotten a jar of vasoline from the tranny seller to make the shafting easier...
Thanks in advance.
big George