Precautions....!! Well There Are Some Letme Mention!!
When Old Engine Is Out And BAY Is Clean......Just Look For Things Inside BAY 1st Which Need Replacement As Its Most Easy Job To Do At A Time.. Letme Mention
Steering Rack....Brake Booster...... Engine Bay PAINT(If Its Rusted And BADly need Paint)
1.Check For Steering Rack...If Power Check For Leaks And Worned Boots And Shaft.....Brake Booster...If You Fell Your Old Booster Is Not Good Enough....Just Replace It Now..As Its 15min Job Now To Fit.....!! After Engine Is Inn Once...Its Hardest Part To Change Them..Minutes Converts Into Hours...Due To lack Of Working Place ...Keep That In Mind...Its My Personal EXperience... 
2.Get Mounts Done From Proper Place....Who's Master In Doing..And Well Known....All Can Make Mounts But Expert Knows The Proper Way To Align Engines.....If Mounts Are Not Done Welll...Axles Issues Can Exist Later Or Vibration Issues In Car....So Look Also For This....!!
3.Same Goes With Wiring....Choose Best Among Town And Also Try Guessing That He's Well Known Enough For JOB's......!! NITTO ELECTRICIANS Are Just Not Enough For This Job...Ur ECM Is Always On Risk In Their Hands....!! So Be Careful....!!
4.Check For Wheel Bearings And Brake Dics(Front) Drums (Rear) And Replace Them Now...While Opening Hubs..Check For Wheel Bearings Too And If Sounding....Also Replace Wheel Bearings....Put New PADS And If Possible Use Some Bigger Discs Available A/c To Spec Of Car Since You Are Going To Put Heavy And More Fast Thing..So Brakes Must Be Perfect....!!
5.A/c To Engine Weight You Need Heavy Front Shocks Too....Diesel Model Shocks Can Do Job As They Are Heavy Enough For Weighty Engines.....If Bought Any Shock From 2nd Hand Market..Just Don't Put Them As They Came.....Remove Springs And Check Either Shock Is In working Condition ..Not Leaking..Or Weak Enough.....!! Checking Will Save Opening Shocks Again And Again In Future....!!
6.Radiator Must Be Big Enough To Cool Down The Engine....Dual Barrel Radiator Is Recommended...!! Do It Once...Swap Dual Barrel Radiator From Any TOYOTA Which Can Fit Or Diesel Models Once...!!
7.Properly Grease Axles And Confirm Axles Are Not Worned....Use Axle GREASE Instead Of Local Or CRAP Grease....It Comes In Tube...Specially For Axles ..One Tube Fills Once...Its JApanese I Think Use It..!!
8..Watever You Swap....Check For Its Service Manual On WEB And Get Oil Specification Of Gearbox Oil And Engine Oil From There...... Using Wrong Oils In Gearbox Can Cause Damage To Synchronizers...So Confirm And Use Correct One....!!
9...Swapping Fuel Pump Inside Fuel Tank Needs Opening Of Tank And Soo....Remember To Get A Bowl Type Square Box Built 1st And Place It Inside Fuel Tank 1st And Swap Pump Base In That Bowl....!! If You Don't...You Will Face Fuel Starvation Issue Later....And Always Use Intank Fuel Pump....Don't Go For Inline (External) Fuel Pumps As They Just Are Easy To Install But Quiet dangerous And Risky As They Get leak......So Make Complete Intank Fuel Pump Setup along With Return Line....!!
10...Swapping Bigger Engines 1NZ-FE/4A-5A-7AFE/4EFE Would Need Bigger Diameter Exhaust Pipe Since A/c To Power Need.....Get Atleast (1 3/4") (45mm) Piping Done From Manifold Till Tail In Order To Make Engine Release Exhaust Easily...!!
Well Thats All I Remember Now And Its Enough For A Successful Swap.....!! Any Thing You Don't Understand...Do Ask For it..
Regards
Farrukh(SER_GTR)