I have recently aquired a 1994 Samurai with 1.3L Fi But the motor is blown. THe body is imaculate no rust anywhere.
I also have an 1988 and a 1986. I blew the motor in the 88 and droped the 86 motor in to it. Both were carb. Now I am going to take the same 1986 Motor and drop it into the 1994 and use the intake from the 1994 for FI. Anything I should concern myself with? anybody do this swap have any info for me?.

1.6L would be a more beneficial swap...

      A 1.6 would be a good swap but would cost you more. Currently you have everything to do the swap with no more to spend  on other things. I have 92 FI sammy and like it hands down over any stock or weber carbed 1.3. I have a 87 engine for back up like you and it would go right in as you say. But you must make a block off plate for the fuel pump. Do it and you will be hooked on Fuel Injection forever, no turning back to funky carbs or crappy webers.

Got it all running today. as far as the block off plate I used the one that was on the original motor from the 1994. For any of you that might do this swap also remeber to remove the push rod for the Fuel pump before you put the cover over it.  I am not sure if it would do any harm but better safe than sorry.  Any ways I got the engine in and running after I went down and purchased a new fuel pump. The vehicle was sitting for 2 years before I got it so I took a chanceand It turned out that the original fuel pump had an internal open.  Purchaced the new pump from Autozone. $150.00  whew.
I remember just buying a new pump for my 88 CArb it was $45.00 Big difference.  Any ways there were a couple of snags I ran into. For some reason when I turn on my ignition  I would not get a ground to the Main relay. This in turn would prevent the Fuel Pump Relay from comming on. I ran a separate ground and now it is ok. Anybody out there Know where the main relay is supposed to get its ground? I think it is fom the ECM  but I am not  sure.

 Fuel pump block off plate? I have a 90 with fuel injection and I don't think that I have seen a plate on it. I thought it looked just like the 1.6 8v head. It would would be a good idea to use a 1.6 short block with your head. If you decide to use your fuel injection setup on another block, you would be better off to find another 1298 instead of using your carburated 1324. There is just enough difference between the two that you will be glad you use a 1298. I've driven a 1.6 8v powered sammy for years with either a stock carb or a weber, loved the power. But, I have just recently been exposed to the injected sammy with a 1298. I was amazed with the horsepower, I think it's close to the 1.6 with the stock carb. Torque is obviously less, but hp is close to the same. It actually gets on with it pretty good!