replacement engines

I was ready to flush my coolant and got this all set up, then noticed coffee colored gunk in the recovery tank. Car never overheated and I checked the fluids 2 days prior and everything was fine. Nothing but oil shows on the dipstick. The check engine light came on briefly a couple of times in the past week, but went out. I will post error codes later today...i hope.
I have a line on a couple of engines for my 145K 2000 boxster s (fear I have a cracked head due to intermix issue) that cost about as much as my repair, plus installation. Question is, I have tiptronic and these are manual. What is involved to use a manual engine and match it to a driving tiptronic? (Meaning I have all the parts for the tiptronic) do I need to switch some stuff over or are the engines just different?
Any help is appreciated.
another question that will help me with diagnostics, how can I test for a cracked head?..I know this could be the oil cooler or o-rings, but feel this is unlikely and hopefully it will be obvious once I tear down into it.