data1 = {{t11,X1},{t12,X2},{t13,X3}, ... ,{t1n,Xn}};
data2 = {{t21,Y1},{t22,Y2},{t23,Y3}, ... ,{t2m,Ym}};

dataClean = Block[
{sTfI, loT, datafrmod, xx, T},
T = 40;

sTfI = Cases[data1, {_, T}][[{1, -1}, 1]];
loT = Select[data1, #[[1]] >= sTfI[[1]] && #[[1]] <= sTfI[[2]] &];

datafrmod = Select[data2, #[[1]] > (loT[[1, 1]] + 5.) && #[[1]]<(loT[[-1, 1]] - 5.) &];
xx = DeleteDuplicates[
Select[loT, #[[2]] != T &][[;; , 1]], (Abs[#1 - #2] < 5. &)];

Do[datafrmod =
Join[Select[datafrmod, #[[1]] < (xx[[i]] - 10) &],
Select[datafrmod, #[[1]] > (xx[[i]] + 10) &]], {i, Length[xx]}];
datafrmod
]; // AbsoluteTiming

data = Block[
{T, which},
T = 40;
which =
With[{tsBad =
Extract[data1[[All, 1]],
Position[data1[[All, 2]], Except[T], {1}, Heads -> False]]},
Complement[Range[Length[data2]], ##] & @@
Nearest[data2[[All, 1]] -> "Index", tsBad, {[Infinity], 10}]];
data2[[which]]
]; // AbsoluteTiming

which = With[{tsBad = Extract[data1[[All, 1]], Position[data1[[All, 2]], Except[T], {1}, Heads -> False]]},
           Complement[Range[Length[data2]], ##] & @@ Nearest[data2[[All, 1]] -> "Index", tsBad, {∞, 10}]];

data3 = data2[[which]];