Hi Bill,
Yes, that's one of the beauties of the TR engine... it's sleeved. That makes it easy to change out the pistons, liners, etc. Easy to "freshen up" and to make size changes, if you wish.
A complete kit of pistons, matching liners, rings and wrist pins is the usual way these engines are rebuilt. Some try just getting pistons/rings/wrist pins and boring the old liners to a larger size, but that's usually not cost effective because the cost of the machine work and the cost of a set with new liners works out close to the same. And the old liners might have cracks/corrosion that make them weaker or less capable of transfering heat out of the cylinder.
In all likelihood, an untouched TR3 would typically be an 83mm bore engine, giving just under 2 liters (that's so the cars would qualify for 2 liter class racing and remained an option on through TR4 at least). With TR4 and TR3"B", 86mm is the most common bore size. That gives just over 2.1 liter. A common upgrade is 87mm, which was the upper limit for racers in the U.S. in certain popular classes in the old days, giving nearly 2.2 liter. Prices on kits for all three of these sizes are roughly the same. I'd venture to guess that most folks rebuilding TR3 go ahead and increase displacement to at least 86mm and often 87mm. After all, more displacment equals more torque and horsepower, so there is little reason not to increase unless the car is being prepped for racing in a class that limits engine size.
More expensive, but possible, is 89mm bore which gives roughly 2.3 liter, in kits that will fit directly into the block without modification. A lot more expensive is up to 92mm bore, getting to around 2.4 liter. But, anything over 89mm requires machine work in the block, for the larger sleeves to fit, and that is the reason it's so expensive.
Visual inspection is just the starting point. With 40-50 year old engine parts, Magnafluxing or other forms of crack detection are a very good idea, especially the crank, conrods and head.
The weakest link in the TR 4-cylinder has to be the conrods. They are drilled and cross-drilled for oil passages and that's where they tend to break. Have a shop pay particular attention to them if you want to reuse. A good engine shop will know how to handle them and prep them. Also be sure to keep the conrods together as a set and matched with their caps. Original conrods in good condition might be considered safe for a daily driver, an engine that seldom sees more than, say, 5000 rpm. But, for higher revving engines an upgrade is probably wise.
One other common issue now is getting the head rebuilt for unleaded fuel. At least, different valves, valve seat inserts and different valve guides are needed. A mistake that seems to be made is boring the replacement valve guides to the original specifications. The new materials in the unleaded fuel guides are more prone to heat expansion than the originals, so really should be honed to be a little on the loose side, perhaps +.0015" on the intake side and +.0025" on the exhaust side. Many modern machine shops don't realize this, but if it's not done, a valve can stick and can in turn pretty quickly destroy a piston and cylinder.
A lot of folks like to install a modern rear crank seal, to help prevent leaks. There are kits available for this purpose from all the major vendors, but be aware that some machining on the crank is necessary, so a good time to prep for a modern seal is while the crank is being reconditioned.
Overall, the TR 4-cylinder is a strong engine and easy to work on. I suggest you consult the factory manual and perhaps some books like Roger Williams "Restoring TR2-4A" and/or Kas Kastner's "TR4/4A Tuning Manual" for lots of useful detail and ideas where the TRactor motor can be improved relatively easily, if you wish. Many of the ideas in both those books take advantage of modern technology and other tuning techniques to build a good perforiming, stronger, more leak- and care-free motor... or a real screamer, if you wish and budget allows! Another good source of info is TeriAnn Wakeman's TR3 restoration website. She details a lot of what was done to her car, including engine work by well-known TR tuner Greg Solow, who is also interviewed for Kas' latest book. TeriAnn's website is
https://www.tjwakeman.net/TR/index.htm
Have fun!