Shift Linkage

[B16 SiRII]

I did a quick search and I didn't find much on my problem, I hope some of you can help me.
I had a cable GSR tranny on the b20b in my 95 hatch and 3rd gear went on it, I bought an LS tranny and used the same shift linkage I had on the GSR. I dropped the GSR put in the LS. I kept the GSR shift linkage (it's all I had) along with the short shifter that was attached, and put it all back together again. On my test run of the tranny I found that 1st and 2nd are perfect, 3rd grinds a bit (but I've never owned a used tranny that didn't grind third under higher rpms on a 6-4 puck clutch.) Additionally, this LS tranny won't go into 4th but it feels like if the shifter could go further down it would engage. 5th goes in smooth but won't come out sometimes unless I pull hard. So did I get screwed on a transmission or did I screw myself by using the GSR shift linkage?

Sorry about the paragraph, but I figure the more I explain the easier it will be to sort out who can help me.
Thanks,
Carlos

[B16 SiRII]

Oh, and I'm using a cable to hydro conversion kit...